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Year 2012 News

Contents:

25-Dec-2012 Happy Holidays
18-Dec-2012 Papers Published
18-Dec-2012 Join the RCSB PDB Team
11-Dec-2012 Map PDB Structures to Full-length Protein Sequences
11-Dec-2012 Announcement: Meeting on Hybrid Methods
04-Dec-2012 Advanced Search: Multiple ID Search
27-Nov-2012 MyPDB: Keep up-to-date with new structures... automatically!
27-Nov-2012 World AIDS Day: December 1
20-Nov-2012 Educational Activities and Lessons
20-Nov-2012 Take our quick survey
13-Nov-2012 Take our quick survey
13-Nov-2012 Ligand Searching
06-Nov-2012 Explore Gallery View of Search Results
30-Oct-2012 Improved Drug Searches and Annotations
23-Oct-2012 New Website Release
16-Oct-2012 Nobel Prize Awarded for studies of G-protein-coupled receptors
16-Oct-2012 Explore the Structural Biology of HIV
09-Oct-2012 Fall Newsletter Published
02-Oct-2012 Advanced Search: Sequence Motif
02-Oct-2012 Turn Your Computer into a PDB Structure Kiosk
25-Sep-2012 Explore PDB Data Overviews
18-Sep-2012 High Resolution Images at the RCSB PDB
11-Sep-2012 Customized Home Page: Structure Comparison Tool
11-Sep-2012 Poster Prize Awarded at ECM
04-Sep-2012 Head Back to School with PDB-101
28-Aug-2012 Smart Searching with the Top Bar Suggestion Box
21-Aug-2012 Download RCSB PDB Mobile for the iPhone/iPad
21-Aug-2012 Poster Prize Awarded at ACA
14-Aug-2012 Improved Ligand Reports
14-Aug-2012 Poster Prize Awarded at ISMB
07-Aug-2012 Build complex queries with Advanced Search
31-Jul-2012 Prepare data for deposition with pdb_extract and SF-Tool
31-Jul-2012 Protein Society Annual Symposium
24-Jul-2012 Upcoming Meeting: ACA
17-Jul-2012 Different Ways To Explore New Entries
10-Jul-2012 ISMB and 3DSIG Meetings
10-Jul-2012 Summer Newsletter Published
03-Jul-2012 Author Profiles: Timeline Display of a Researcher's Structures
26-Jun-2012 Latest Website Release
19-Jun-2012 Personalize the RCSB PDB with MyPDB
19-Jun-2012 National Protein Modeling Champions
12-Jun-2012 Top Bar SMILES String Searching
05-Jun-2012 Molecule of the Month reaches 150
29-May-2012 Tour the PDB with Drill-down Pie Charts
22-May-2012 Domain-based Structural Alignments
15-May-2012 New Poster: Virus Structures
08-May-2012 Bookmark and Post Webpages
08-May-2012 Customized Home Page: Sequence Search
01-May-2012 Latest Website Release
24-Apr-2012 Rutgers Day (April 28)
24-Apr-2012 Create a Collage of Structures
17-Apr-2012 DNA Day 2012: April 20
17-Apr-2012 Exhibiting at Experimental Biology
10-Apr-2012 Spring Newsletter Published
03-Apr-2012 Depositing Structures with Ligands
27-Mar-2012 Browse the PDB by GO Terms, EC Number, Source Organism, and More
20-Mar-2012 Visit the San Diego Festival of Science and Engineering on March 24
20-Mar-2012 J.P. Stevens HS Wins NJ Protein Modeling Event
13-Mar-2012 Sound Science
13-Mar-2012 Preview New 3D Similarity Tab
13-Mar-2012 PDBMobile and iOS 5.1
06-Mar-2012 Explore a Structural View of Biology at PDB-101
28-Feb-2012 Visualize Molecular Surfaces with Protein Workshop
21-Feb-2012 Visit the Biomolecular Discovery Dome at Biophysical Society
21-Feb-2012 New Structures Widget
14-Feb-2012 Ligand Summary Pages
07-Feb-2012 Volunteer Structures For Foldit
07-Feb-2012 Free Webinar and Updated Tutorial
31-Jan-2012 Announcement: Meeting on Hybrid Methods
31-Jan-2012 Free Webinar on How to use the RCSB PDB
24-Jan-2012 Newsletter Published
17-Jan-2012 NJ Science Olympiad Protein Modeling Results
10-Jan-2012 Web Services for Accessing PDB Data
03-Jan-2012 Annual Report Published

Earlier news is available and is archived in the RCSB PDB newsletters.


25-Dec-2012

Happy Holidays

A structural view of the citric acid cycle, highlighted in the October 2012 Molecule of the Month, is shown.

A structural view of the citric acid cycle, highlighted in the October 2012 Molecule of the Month, is shown.

For RCSB PDB highlights from the past year, please download the 2012 Annual Report (PDF).

18-Dec-2012

Papers Published

Articles covering a variety of topics have been published:

  • The RCSB Protein Data Bank: new resources for research and education (2013) Nucleic Acids Research doi: 10.1093/nar/gks1200

Update of new tools and resources that provide a structural view of biology for research and education, including improved methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments.

  • Creating a community resource for protein science (2012) Protein Science 21: 1587-1596 doi: 10.1002/pro.2154

Discusses how management, data content, infrastructure, and community have influenced the continued development of the PDB. It also analyzes the corpus of data to identify trends in the field of structural biology.

Describes modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

  • Illustrating the Machinery of Life: Viruses (2012) Biochemistry and Molecular Biology Education 40: 291-296 doi: 10.1002/bmb.20636

David Goodsell's series continues with illustrations of poliovirus, influenza, and HIV.

David Goodsell describes his thoughts and process for scientific illustrations.

A list of all RCSB PDB articles is available from the Publications page.

18-Dec-2012

Join the RCSB PDB Team

The RCSB PDB is looking for a Lead Web Architect.

11-Dec-2012

Map PDB Structures to Full-length Protein Sequences

Protein Feature View from 2vx3's Structure Summary page.

(Click image to enlarge)
Protein Feature View from 2vx3's Structure Summary page.

The new Protein Feature View visually summarizes how a full-length protein sequence from UniProtKB corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are also displayed.

Protein Feature View for all entries with UniProtKB ID Q13627.  This image can be exported as an SVG file.
Protein Feature View for all entries with UniProtKB ID Q13627.  This image can be exported as an SVG file.

For individual entries, the Protein Feature View is available from the Molecular Description Widget on Structure Summary pages.  The example shown for PDB ID 2vx3 illustrates how the ranges of a protein that have been observed in an experiment (in blue) correspond to the full length UniProtKB sequence (in grey). The secondary structure information from the PDB entry is also shown (helices in red, beta strands in yellow).

Various features that are known for the UniProtKB sequence are displayed in green as they correlate with regions in the PDB entry. Active sites (from UniProtKB and the PDB entry) are also annotated. Moving the mouse cursor over the "lollipops" displays the residue label. Mousing over the images shown in the "Secstruc" row reveals secondary structure from the PDB entry.

This view can be expanded to map all PDB entries related to a single UniProtKB sequence by selecting the Protein Feature View link shown in this widget. By default, a few representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available. Selecting the plus sign or the "Show All" button will expand the view to show all related PDB chains, which can then be sorted by resolution, length, and release date. These Protein View images can be exported as Scalable Vector Graphics (SVG) files.

The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

11-Dec-2012

Announcement: Meeting on Hybrid Methods

Meeting Flyer.

(Click image to open flyer)
Meeting Flyer.
Dynein cargo transport by Graham Johnson
Dynein cargo transport by Graham Johnson

A conference on the Structural Analysis of Supramolecular Assemblies by Hybrid Methods will take place March 3-7, 2013 at Granlibakken Resort in Tahoe City, California, USA.

Organized by Andrej Sali (University of California, San Francisco), Brian T. Chait (Rockefeller University), and David Baker (University of Washington), the three-day conference will:

  • Convene with a keynote address by Peter Walter (University of California, San Francisco), followed by three days of stimulating plenary sessions, workshops/panels and poster sessions;
  • Highlight the strengths and limitations of the current hybrid approaches for analyzing cellular and molecular structures (X-ray crystallography, NMR spectroscopy, electron microscopy, small angle X-ray scattering, mass spectrometry, chemical cross-linking, super-high resolution optical microscopy, optical microscopy and others);
  • Identify promising new advances in experimental methods for
    collecting the data and computational methods for converting the data to
    models.

Scholarships are available to students and postdocs and require submission of a brief application and abstract. Short talks will also be selected from submitted abstracts. Discounts for students and early registrations are available. For more information, see www.keystonesymposia.org/13C1.

04-Dec-2012

Advanced Search: Multiple ID Search

Have a list of PDB IDs you'd like to learn more about?  Use Advanced Search to view all of the structures in the Query Results Browser.
Have a list of PDB IDs you'd like to learn more about?  Use Advanced Search to view all of the structures in the Query Results Browser.
Enter a list of PDB IDs into the Advanced Search.

(Click image to enlarge)
Enter a list of PDB IDs into the Advanced Search form.

Have a list of PDB IDs you'd like to learn more about? Use Advanced Search to view all of the structures in the Query Results Browser.

From the Advanced Search pulldown menu, select ID(s) and Keywords>PDB ID(s). Enter the list of multiple IDs, which can be separated by commas or white space, including line breaks.

The structures can then be explored using the different query results browser views: detailed, condensed, timeline or gallery.

Users can also link directly to multiple structures in the Query Results Browser using the syntax:
http://www.rcsb.org/pdb/search/smart.do?smartSearchSubtype_1=StructureIdQuery&structureIdList_1=1MI6+1MVR

This example will launch entries 1mi6 and 1mvr in the Query Results Browser; other IDs can be added to the URL:
http://www.rcsb.org/pdb/search/smart.do?smartSearchSubtype_1=StructureIdQuery&structureIdList_1=1MI6+1MVR+4GMK+4GSB

27-Nov-2012

MyPDB: Keep up-to-date with new structures... automatically!

MyPDB will email alerts when structures matching saved queries are released.
(Click image to enlarge)
MyPDB will email alerts when structures matching saved queries are released.
Users add entries to a MyPDB bookmark list of entries, and add personal text annotations.
(Click image to enlarge)
Users add entries to a MyPDB bookmark list of entries, and add personal text annotations.

Create a personalized version of the RCSB PDB website using these MyPDB features:

  • Sign up for regular email alerts. Searches saved in MyPDB can be set to run with each update. Email alerts (weekly or monthly) will be sent when new entries matching the search are released in the PDB archive.
  • Save searches online. The MyPDB Saved Query Manager stores any type of RCSB PDB structure search - a particular keyword, sequence, ligand, Advanced Search composite query, and more. Run these searches at any time with the click of a button.
  • Store personal notes and bookmark structures. Save personal annotations and notes on the Structure Summary tab of any PDB entry. Want to keep a running list of interesting structures? MyPDB can keep a favorites list of PDB entries. The Personal Annotations summary page provides easy access to all of these tagged structures and annotations.

All MyPDB account information is kept private and secure, and can be updated at any time.

27-Nov-2012

World AIDS Day: December 1

HIV (human immunodeficiency virus) is composed of two strands of RNA, 15
types of viral proteins, and a few proteins from the last host cell it
infected, all surrounded by a lipid bilayer membrane. Together, these
molecules allow the virus to infect cells of the immune system and force
them to build new copies of the virus. Each molecule in the virus plays
a role in this process, from the first steps of viral attachment to the
final process of budding.
(Click image to enlarge)
HIV (human immunodeficiency virus) is composed of two strands of RNA, 15 types of viral proteins, and a few proteins from the last host cell it infected, all surrounded by a lipid bilayer membrane. Together, these molecules allow the virus to infect cells of the immune system and force them to build new copies of the virus. Each molecule in the virus plays a role in this process, from the first steps of viral attachment to the final process of budding.

World AIDS Day, observed each year on December 1, raises awareness of the AIDS pandemic caused by the spread of HIV infection. The theme for 2012 is Working Together for an AIDS-Free Generation.
To learn more, visit www.worldaidsday.org and aids.gov.

Structural biologists have been actively studying HIV-related proteins and drugs. Since 1987, the NIH has sponsored annual meetings to discuss the progress made in this field.  In 2011, a poster (and related animation) was created to commemorate the NIGMS's 25th Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and Their Application to Targeted Drug Design. The poster, available for download from PDB-101, highlights the examples of the structural proteins, viral enzymes, and accessory proteins of HIV that are available in the PDB archive.

HIV protease is one of the most frequently-deposited proteins, with  almost 500 entries currently in the archive. Around half of these entries are bound to a drug or inhibitor.

Other related RCSB PDB resources include Molecule of the Month features on HIV protease, integrase, and reverse transcriptase.

20-Nov-2012

Educational Activities and Lessons

PDB-101 offers different activities for learning about structures in the PDB.

(Click image to enlarge)
PDB-101 offers different activities for learning about structures in the PDB.

The PDB-101 website packages together resources that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.

The Educational Resources section of PDB-101 offers different materials to help learn about structures in the PDB, including posters, animations, and classroom activities and lessons.

These activities and lessons include:

  • Exploring the Structure of tRNA. Build a paper model of the primary, secondary, and beginnings of the tertiary structure of tRNA. Visit the related activity page to learn more.
  • Virus Structure Lecture, Lesson Plans, and Activities. These resources, aimed at middle and high school classrooms, include templates to make 3D paper models of disease-causing viruses and review questions.
  • Green Fluorescent Protein Tutorial. With this tutorial you will find protein structures using search tools on the RCSB PDB website; use molecular visualization tools to explore the GFP structure and function; and find the GFP gene and view important mutations.
  • 3D Paper Model of DNA. Download this PDF to build one complete turn of a DNA double helix, with the major and minor grooves labeled. 
  • Education Corner. Other activities and lessons are available from the RCSB PDB Newsletter's Education Corner archives.

To enter this educational view of the RCSB PDB, click on the blackboard PDB-101 logo or its related widget in the left-hand menu. PDB-101 offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the upper-left PDB-101 pulldown menu to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website.

20-Nov-2012

Take our quick survey

If you haven't already done so, please answer a few, brief questions to help us learn about our users. Your responses are greatly appreciated!

13-Nov-2012

Take our quick survey

Survey logo.

Please answer a few, brief questions to help us learn about our users. Your responses are greatly appreciated!

13-Nov-2012

Ligand Searching

Learn more about the the active form of vitamin D found in the body (ID: VDX) in November's Molecule of the Month feature.

(Click image to enlarge)
Learn more about the the active form of vitamin D found in the body (ID: VDX) in November's Molecule of the Month feature.

Quickly find small molecule components found in PDB entries using any of these tools:

  • Simple top bar searching (with autocomplete suggestions)

Click on the Ligand icon to limit your search. Enter a ligand name or the 3-character chemical component ID.

Chemical Component Search.

This powerful form can be accessed by selecting the top bar ligand icon and then [ additional ligand options ]. Launch the chemical structure editor to draw a structure, or paste in a SMILES or SMARTS string, and then perform a substructure, exact, similarity, or superstructure search. In addition, ligands can be searched by name, identifier, formula, and molecular weight.  A tutorial demonstrating this search is available.

Advanced Search.

Supports the searches mentioned above, as well as queries by chemical component type, binding affinity, sub-component, and more. These types of searches can be combined and even amended with searches for the associated structures. Learn more about Advanced Search with this tutorial and list of available queries.

Ligand searches return the corresponding Ligand Summary page that contains an overview of the chemical component, 2D and 3D images, links to other resources, and links to related ligands and PDB entries.

All residues and small molecule components found in PDB entries, including standard and modified amino acids/nucleotides, small molecule ligands, ions, and solvent molecules, are described in the wwPDB's Chemical Component Dictionary.

06-Nov-2012

Explore Gallery View of Search Results

Gallery view for a search for cAMP-dependent protein kinase structures.  Images can be resized, and entries can be selected or deselected.
(Click image to enlarge)
Gallery view for a search for cAMP-dependent protein kinase structures.  Images can be resized, and entries can be selected or deselected.

In addition to the original query results browser, now called the detailed view, results can be browsed using condensed, timeline or gallery views. The views are synchronized; selecting or deselecting a structure in one view will have the same effect in the others.

From the initial search results, select View>Gallery to display any search result set as a series of tiled molecular pictures. Moving your mouse over each image in the collage displays the structure title; clicking on the small image shows a larger version. The PDB ID listed links to the corresponding Structure Summary page; the PDB IDs can also be hidden from the gallery.

This feature was added as part of the latest website release.

30-Oct-2012

Improved Drug Searches and Annotations

The Ligand Summary Drug Info widget lists and links to corresponding data from DrugBank (when available), including DrugBank ID, drug name, groups, brand name, descriptions, and more.
(Click image to enlarge)
The Ligand Summary Drug Info widget lists and links to corresponding data from DrugBank (when available), including DrugBank ID, drug name, groups, brand name, descriptions, and more.
PDB-101 offers downloads of a poster and a flyer called How Do Drugs Work? that explore different kinds of protein-drug structures found in the PDB archive.

PDB-101 offers downloads of a poster and a flyer called How Do Drugs Work? that explore different kinds of protein-drug structures found in the PDB archive.

Drug and drug target data from DrugBank (www.drugbank.ca) have been integrated with the RCSB PDB website.

The simple top bar search can find generic and brand names of drugs. For example, type Zoloft into the simple top bar search to find the related Ligand Summary page.

The Ligand Summary page links to entries containing Zoloft and provides summary information about the drug. The Drug Info widget on this page lists and links to corresponding data from Drugbank (when available), including DrugBank ID, drug name, groups, brand name, descriptions, and more.

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. C. Knox, V. Law, T. Jewison, P. Liu, S. Ly, A. Frolkis, A. Pon, K. Banco, C. Mak, V. Neveu, Y. Djoumbou, R. Eisner, A.C. Guo, D.S. Wishart (2011) Nucleic Acids Res. 39:D1035-41. DOI: 10.1093/nar/gkq1126

23-Oct-2012

New Website Release

Explore query results through four different views: detailed, condensed, image gallery, and timeline.
(Click image to enlarge)
Explore query results through four different views: detailed, condensed, image gallery, and timeline.

New and enhanced features have been added to the RCSB PDB, including:

The new Protein Feature View provides a graphical summary of UniProt sequence features and their relationship with PDB entries.
(Click image to enlarge)
The new Protein Feature View provides a graphical summary of UniProt sequence features and their relationship with PDB entries.
  • The Protein Feature View provides a graphical summary of how a sequence from UniProtKB corresponds to PDB entries. The view loads annotations from external databases, models from the Protein Model Portal, and more. This feature is launched from the Molecular Description widget found on Structure Summary pages. View an example Protein Feature View launched from PDB entry 2vx3 here.

  • Simple Macromolecule Name Searches from the top menu bar have been improved. Searches now cross-reference polyproteins and multi-component proteins with PDB entities based on alignment and residue ranges from UniProtKB. For example, a search for "Gag-Pol" suggests retrieving all Gag-Pol polyprotein structures or those for a particular component (protease, reverse transcriptase, integrase, etc.)


  • Drug and drug target data from DrugBank have been integrated with the RCSB PDB website. The top bar simple search suggests generic and brand names of drugs. A Drug Info widget on the Ligand Summary pages lists the corresponding data from Drugbank (when available). The widget contains DrugBank ID, drug name, groups, brand name, and more, with links to the corresponding DrugBank data.


  • To help users browse search results, new options have been added. In addition to the original results browser, now called the "detailed view," we have added a condensed view, a new gallery view, and a timeline view. The views are synchronized; selecting or deselecting a structure in one view will have the same effect in the others.


  • External links to AtlasCBS have been added to the Link tab for Structure Summary pages. AtlasCBS is a web server to map and explore chemico-biological space.


See the What's New page for more new features and examples.

16-Oct-2012

Nobel Prize Awarded for studies of G-protein-coupled receptors

G-Protein Coupled Receptors: 
In honor of the 2012 Nobel Prize in Chemistry.
(Click image to download the flyer)
G-Protein Coupled Receptors
In honor of the 2012 Nobel Prize in Chemistry.
The 2012 Nobel Prize in Chemistry was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka for studies of G-protein-coupled receptors. The PDB holds many GPCRs, such as Kobilka's groundbreaking structure of the beta2 adrenergic receptor-Gs protein complex shown on this commemorative flyer (PDF).

To learn more about GPCRs, see the Molecule of the Month articles on Adrenergic Receptors and G Proteins, and the Author Profile for Brian Kobilka.

16-Oct-2012

Explore the Structural Biology of HIV

Learn about HIV with a PDB-101 poster and interactive animation.
(Click image to enlarge)
Learn about HIV with a PDB-101 poster and interactive animation.

HIV (human immunodeficiency virus) is composed of two strands of RNA, 15 types of viral proteins, and a few proteins from the last host cell it infected, all surrounded by a lipid bilayer membrane. Together, these molecules allow the virus to infect cells of the immune system and force them to build new copies of the virus. Each molecule in the virus plays a role in this process, from the first steps of viral attachment to the final process of budding.

The structural proteins, viral enzymes, and accessory proteins of HIV that have been determined are highlighted in a downloadable poster and an interactive, online Flash website. Clicking on a protein in the animation reveals information about the structure and a link to the PDB entry.

For more information about the HIV virus, see the Molecule of the Month features on HIV protease, integrase, and reverse transcriptase.

09-Oct-2012

Fall Newsletter Published

Fall 2012 Newsletter.
(Click image to open newsletter)
Fall 2012 Newsletter.

The fall 2012 issue (HTML | PDF) has been published.

The newsletter describes how to head back to school with the educational materials from the PDB-101 website. Features include Author Profiles and a new tRNA model building activity.

Deposition articles discuss how to prepare data submissions using pdb_extract and SF-Tool, and 2012 deposition statistics.

Features related to Data Query, Reporting, and Access highlight RCSB PDB Mobile, smart searching, PDB Data Overviews, and more.

The Outreach and Education section announces the 2012 RCSB PDB Poster Prize awardees and describes how to create high resolution molecular images.

The Education Corner, by John Rose, Wendy Dustman, and Julie Kittleson, looks at the University of Georgia's Biotech Boot Camp for high school teachers.

This quarterly newsletter is published online and in print. Past issues are available. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

02-Oct-2012

Advanced Search: Sequence Motif

The RCSB PDB's Advanced Search lets users build queries of specific types of data. To look for structures with a particular Sequence Motif, try using one of these techniques with the Sequence Features>Sequence Motif option. A Sequence Motif can be an exact sequence or a sequence pattern expressed by regular expression syntax. Regular expressions are powerful notations for defining complex sequence patterns. Click on the sequence to run the example queries:

  •   Short Sequence Fragments

Use the sequence motif search to search for short sequence fragments of any size, such as NPPTP

  •   Wildcard Searches

Use an 'X' in the sequence for wildcard searching.  For example, XPPXP can be entered to look for SH3 domains using the consequence sequence -X-P-P-X-P (where X is a variable residue and P is Proline)

  •   Multiples of Variable Residues

The {n} notation can be used, where n is the number of variable residues. To query a motif with 7 variables between residues W and G, and 20 variable residues between G and L, try WX{7}GX{20}L

  •   Ranges of Variable Residues

The {n,m} notation can be used to indicate ranges of variable residues, where n is the minimum and m the maximum number of repetitions. For example the zinc finger motif that binds Zn in a DNA-binding domain can be expressed as CX{2,4}CX{12}HX{3,5}H

  •   Motifs at the Beginning of a Sequence

The '^' operator searches for sequence motifs at the beginning of a protein sequence. Two ways of looking for sequences with N-terminal histidine tags are ^HHHHHH and ^H{6}

  •   Alternative Residues  

Square brackets specify alternative residues at a particular position. To search for a Walker (P loop) motif that binds ATP or GTP, use [AG]XXXXGK[ST]

The search will look for sequences with A or G, followed by 4 variable residues, then G K, and finally S or T.

02-Oct-2012

Turn Your Computer into a PDB Structure Kiosk

kiosk logo

Kiosk logo

Highlight structures from your lab, institution, or class with the Molecules in Motion Kiosk Viewer. Using a list of PDB IDs, this full-screen animation program will display any structure from different angles and perspectives. It also focuses on any chemical components within the structure. The Java viewer can be downloaded or launched from the Educational Resources page, or by using the form below.

Launch Kiosk by providing a comma separated list of PDB ids: (Java required)


By default Kiosk will display biological assemblies (if available). Uncheck here to view asymmetric units only.

25-Sep-2012

Explore PDB Data Overviews

PDB Data  Overviews.
(Click image to enlarge)
PDB Data  Overviews.

The RCSB PDB maintains several lists that display PDB data in interesting and useful ways. Highlights include:

This page lists clusters of proteins (with greater than 95% sequence similarity) containing at least one structure solved by one method (e.g. X-ray) and one by a different method (e.g. NMR).

View histograms of the PDB archive based on characteristics like space group, journal, Enzyme Classification, and more. The growth of the number of PDB entries released per year is organized around experimental method, molecule type, and unique protein classifications. Data can be downloaded as Excel documents.

Subscribe to RSS feeds to access the latest structures (from the RCSB PDB) and Molecule of the Month articles (from PDB-101) as soon as they become available.

Links to summary files available from the PDB FTP, including a file with all PDB sequences in FASTA format; one with all PDB IDs, molecule type, and experimental method; and one with all PDB IDs and authors.

A FASTA formatted file generated using DSSP displays sequences and secondary structure for all entries. A separate file includes notation of regions which have not been experimentally observed in addition to the secondary structure.

The top right of every RCSB PDB page header links to the full archive (select the number of total structures) and to the entries in the most recent update (select the date listed).

Author Profiles vertically display structures associated with a particular researcher. Profiles are also available for Structural Genomics centers.

Articles are indexed by title, date, and category, and accessible from an alphabetical pull-down menu.

18-Sep-2012

High Resolution Images at the RCSB PDB

Pyruvate Dehydrogenase Complex image

Download high resolution image

Images from the Molecule of the Month, such as this Pyruvate Dehydrogenase Complex, can be downloaded as high resolution TIFF files.

Citation and usage information

Create or download publication-quality pictures of biomacromolecules with the RCSB PDB.

Image of 3izi created using Protein Workshop
Download high resolution image

Image of 3izi created using Protein Workshop

Several interactive, Java-based tools1 can be used to visualize PDB data and create pictures.  Protein Workshop offers easily customized views; Simple Viewer utilizes a quick ribbon display; and Ligand Explorer visualizes the interactions of bound ligands in protein and nucleic acids structures.

Each program can be used to create and save high-resolution images in JPEG, PNG, and TIFF formats. Using the Save Image dialog box from the File menu, users can specify the width and height of an image in pixels, inches, or millimeters.

From the educational PDB-101 site, high resolution TIFFs used to illustrate Molecule of the Month articles can be downloaded and used in presentations and publications (see citation and usage information). The high resolution files are linked from each article, and available as an archive.

PDB-101 posters, including The Structural Biology of HIV and Molecular Machinery: A Tour of the Protein Data Bank, can be saved as high or low resolution PDFs.

1J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications BMC Bioinformatics 6:21.

11-Sep-2012

Customized Home Page: Structure Comparison Tool

Use the Customize This Page option from the left menu to select widgets to appear on the RCSB PDB home page.
(Click image to enlarge)
Use the Customize This Page option from the left menu to select widgets to appear on the RCSB PDB home page.

The RCSB PDB homepage is comprised of web widgets that can be moved around, minimized, or hidden so users can create a website that reflects their interests. Frequently-used features can be moved to the top, while less popular items can be hidden or collapsed.

The Structure Comparison Tool widget can be added to the home page.  All widgets with a dark blue bar on top can be moved around on the page by dragging the arrow buttons.
(Click image to enlarge)
The Structure Comparison Tool widget can be added to the home page.  All widgets with a dark blue bar on top can be moved around on the page by dragging the arrow buttons.

The Structure Comparison Tool widget can be added so that it appears every visit to the RCSB PDB home page. The tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, Mammoth, TM-Align, TopMatch).

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) and detection of circular permutations (via jCE).

To add this widget to the RCSB PDB home page, select the Customize This Page button from the left menu. Download Files, Sequence Search, and ADIT Deposition widgets can also be added or removed.

The Comparison Tool is also available as a web page and as a standalone Java Web Start application. Additional information is available online and as a flyer (PDF).

11-Sep-2012

Poster Prize Awarded at ECM

Congratulations to Jonas Lindholt for Cardiotonic Steroids and the Na/K-ATPase.

Congratulations to Jonas Lindholt for Cardiotonic Steroids and the Na/K-ATPase.
ECM logo.

The RCSB PDB Poster Prize at the 2012 European Crystallographic Meeting (ECM, August 7-11, Bergen, Norway) went to Jonas Lindholt for

Cardiotonic Steroids and the Na/K-ATPase
Jonas Lindholt, Linda Reinhard, Poul Nissen
Centre for Membrane Pumps in Cells and Disease (PUMPkin) and Department of Molecular Biology and Genetics, Aarhus University, Denmark

Jonas will receive the Machinery of Life by David S. Goodsell and International Tables Volume A/Space-group symmetry.

Many thanks to Andreas Roodt (ECM Prize Committee and University of the Free State, South Africa), the  European Crystallographic Association, and the judges: Udo Heineman (Max-Delbr¯ck Center for Molecular Medicine, Berlin), Linda Shimon (Weizmann Institute of Science), and Ute Krengel (University of Oslo).

All 2012 awardees will be listed on the RCSB PDB website.

04-Sep-2012

Head Back to School with PDB-101

Learn about the structure and function of tRNA by building a paper model in this new PDB-101 activity.

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Learn about the structure and function of tRNA by building a paper model in this new PDB-101 activity.

The PDB-101 website packages together resources that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.  Major topics include:

  • Author Profiles are a unique historical and educational tool that display a timeline of the structures associated with a particular researcher.  Example profiles and searches for authors and structural genomics centers are available.
  • Molecule of the Month articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.  Each feature can be accessed from a pull-down menu or from the archive.
  • Understanding PDB Data is a reference to help explore and interpret individual PDB entries. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges to exploring the archive.

To enter this educational view of the RCSB PDB, click on the blackboard PDB-101 logo or its related widget in the left-hand menu. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the upper-left PDB-101 pulldown menu to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website.

28-Aug-2012

Smart Searching with the Top Bar Suggestion Box

Enter text in the top search bar to quickly find structures based on author, macromolecule name, sequence, ligand, and more.
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Enter text in the top search bar to quickly find structures based on author, macromolecule name, sequence, ligand, and more.

The top menu bar recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.

Simple text searches complement other RCSB PDB tools: the Explore Archive widget provides browsable data distribution summaries, Browse Database explores the PDB archive using different hierarchical trees, and Advanced Search combines multiple searches of specific types of data.
(Click image to enlarge)
Simple text searches complement other RCSB PDB tools: the Explore Archive widget provides browsable data distribution summaries, Browse Database explores the PDB archive using different hierarchical trees, and Advanced Search combines multiple searches of specific types of data.

The top search bar helps users easily and intuitively create simple text searches.

Typing text in the top search bar launches an interactive pop-up box that suggests possible matches that are organized by categories ranging from author name to ontology terms. The top search can be also be limited to quick searches on Author, Macromolecule name, Sequence, or Ligand by selecting the related icon.

The top menu bar recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.
(Click image to enlarge)
The top menu bar recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.

Using these categories helps to quickly differentiate between possible search results.

For example, autosuggestions for the input bird include authors whose names contain "bird" and structures from the organism bird.

Users who want to perform a simple, non-categorized text search can click the magnifying glass icon or press return.

The top menu bar also recognizes particular types of syntax. Entering SMILES strings will suggest options to perform substructure, exact structure, or similar chemical structure searches, while typing in a sequence will offer different BLAST search options.

Simple text searches complement other RCSB PDB tools: the Explore Archive widget provides browsable data distribution summaries, Browse Database explores the PDB archive using different hierarchical trees, and Advanced Search combines multiple searches of specific types of data.

21-Aug-2012

Download RCSB PDB Mobile for the iPhone/iPad

Search the PDB, access MyPDB, view molecules in 3D, and more.
(Click image to enlarge)
Search the PDB, access MyPDB, view molecules in 3D, and more.

The new RCSB PDB app provides fast, on-the-go access. Search the entire PDB, view the latest weekly release of structures, access your MyPDB account, view the entire catalog of Molecule of the Month articles, and more using either a WiFi or cellular data connection and an iPad/iPhone device. Click on the App Store icon below to access the free download of RCSB PDB Mobile.

Click on the App Store link to access the free download of RCSB PDB Mobile.

The latest release improves upon the 3D display of macromolecular biomolecules.

Further information is available from the RCSB PDB Mobile information page, PDF flyer, and FAQ. RCSB PDB Mobile is an update of the beta-tested PDBMobile.

A version of the app for the Android platform is in development.

21-Aug-2012

Poster Prize Awarded at ACA

Sergei Kalynych.
(Click image to enlarge)
Sergei Kalynych.
Rebecca Goldstein.
(Click image to enlarge)
Rebecca Goldstein.
ACA, July 28-August 1; Boston, MA.
ACA, July 28-August 1; Boston, MA.

The RCSB PDB Poster Prize at the 2012 Meeting of the American Crystallographic Association (ACA, July 28-August 1; Boston, MA), went to Sergei Kalynych for Crystallographic studies of closely related lipopolysaccharide O-antigen chain length regulators
Sergei Kalynych,1 Deqiang Yao,2 James Magee,1 Mirek Cygler2
1McGill University, 2University of Saskatchewan

Sergei will receive a subscription to Science and a copy of a book of his choice.

An honorable mention was awarded to Rebecca Goldstein for A possible mechanism for the regulation of the PI-PLC from S. aureus
Rebecca Goldstein, Jiongjia Cheng, Mary Roberts, Boston College.

Many thanks to the judges: Barry Finzel (Chair, University of Minnesota), Patrick Loll (Drexel University), and David Rose (University of Waterloo), and to Marcia Colquhoun and the ACA.

All 2012 awardees will be listed on the RCSB PDB website.

14-Aug-2012

Improved Ligand Reports

Ligand Summary Reports include information about the selected chemical components such as formula, molecular weight, name, SMILES string, which PDB entries are related to the ligand, and how they are related.

Generate Reports: Ligand Summary

To generate a report, select the Ligand Summary option from the Generate Reports pull-down menu for any set of query results.


Click on the triangle to reveal the sub-table of PDB IDs.

For each ligand included in the report, a sub-table can be selected to show lists of all related PDB entries that contain the ligand, the entries that contain the ligand as a free ligand, and entries that contain the ligand as part of a larger, polymeric ligand.

To display this sub-table, select the triangle shown next to the Ligand ID. The display is limited to 15 PDB IDs in each column. For ligands associated with more than 15 PDB entries, the ... [more] link will launch a query for that set of structures.

All tabular report features are also available, including sorting, filtering, export to other report formats, and column customization.

Ligands can also be displayed as an image collage.

14-Aug-2012

Poster Prize Awarded at ISMB

Congratulations to Alan Barber for Evolution of function in the alkaline phosphatase superfamily.

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Congratulations to Alan Barber for Evolution of function in the alkaline phosphatase superfamily.

The RCSB PDB Poster Prize at the 2012 Conference on Intelligent Systems for Molecular Biology (ISMB, July 15-17, Long Beach, CA) went to Alan Barber for

ISMB 2012.

Evolution of function in the alkaline phosphatase superfamily
Alan Barber,1 Jonathan Lassila,2 Helen Wiersma-Koch,2 Michael Hicks,1 Daniel Herschlag,2 Patricia Babbitt1
1University of California, San Francisco, 2Stanford University

Alan will receive a subscription to Science and a copy of Structural Bioinformatics: An Algorithmic Approach by Forbes J. Burkowski

Many thanks to the Steven Leard, the International Society for Computational Biology, and the judges: Yana Bromberg (Chair, Rutgers), Hannah Carter (Johns Hopkins), Jeroen deRidder (Delft University of Technology), Iddo Friedberg (Miami University, Oxford, Ohio), Tatyana Goldberg (Technical University Munich, Germany), Ben Jelen (Rutgers), Hande Kucuk (University of Miami), Biao Li (Buck Institute, Novato), Magali Michaut (Netherlands Cancer Institute), Yanay Ofran (Bar Ilan University), Susanna Repo (EMBL-EBI), Venkata Satagopam (EMBL-Heidelberg), Andrea Schafferhans (Technical University Munich), Avner Schlessinger (UCSF), Stefan Senn (Rutgers), Janita Thusberg (Buck Institute, Novato), Tobias Wittkop (Buck Institute, Novato), Chengsheng Zhu (Rutgers).

All 2012 awardees will be listed on the RCSB PDB website.

07-Aug-2012

Build complex queries with Advanced Search

Click on the magnifying glass icon from the top menu bar to access Advanced Search.
Click on the magnifying glass icon from the top menu bar to access Advanced Search.

Advanced Search provides the capability of combining multiple searches of specific types of data in a logical AND or OR. The result is a list of structures that comply with ALL or ANY of the search criteria, respectively.

Individual data items are organized by category; contextual help and examples are available by selecting  . New options include quick searches by experimental and/or molecule type, searches based on structure determination method, and the ability to find structures containing interresidue connectivity (LINK records) that cannot be inferred from the primary structure.

Currently, users can build searches based on:

  • Quick Search: retrieve all PDB entries or a subset based on experimental method or molecule type
  • ID(s) and Keywords: PDB, PubMed, UniProtKB, Pfam IDs; text and keyword searching
  • Structure Annotation: structure title, description; and macromolecule name
  • Deposition: author name; deposit, release, and revision date; latest released and modified structures; Structural Genomics Project
  • Structure Features: macromolecule type; number of chains (asymmetric unit or biological assembly), entities, models, and disulfide bonds; interresidue connectivity (LINK records); molecular weight; secondary structure content; secondary structure length; SCOP, CATH, taxonomy
  • Sequence Features: sequence; translated nucleotide sequence; sequence motif; chain length; genome location
  • Chemical Components: name; ID; InChi descriptor; SMILES/SMARTS; molecular weight; chemical formula; chemical component type; binding affinity; has ligands; has modified residues; sub-components
  • Biology: Source; expression organism; Enzyme Classification; biological process; cell component; molecular function; Transporter Classification
  • Methods: experimental method; X-ray resolution, R factor, diffraction source, structure determination method, reflections, cell dimensions, software, space group, crystal properties, detector; EM assembly
  • Publication: citation; MeSH terms; PubMed abstract
  • Misc: Has external links

The number of entries matching each individual query can be shown before running the full Advanced Search.  Searches can also be filtered by removing sequence similarity.

Advanced Searches can be stored in MyPDB to be run or modified at any time.

31-Jul-2012

Prepare data for deposition with pdb_extract and SF-Tool

Image created at www.wordle.net

(Click image to enlarge)
Image created at www.wordle.net.

Tools are available to help prepare data files for deposition with ADIT. Using these resources can help minimize errors, validate data, and save time during the deposition process.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications.

pdb_extract extracts key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into mmCIF data files that can be used with ADIT for validation and deposition.

Features include support for:

  • Data from hybrid method experiments
  • NCS and TLS ranges in BUSTER and REFMAC
  • Improved mtz to mmCIF conversion
  • Quality assessment of X-ray data

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org.  

SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.

Visit sf-tool.rcsb.org to:

SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.

(Click image to enlarge)
SF-Tool is a streamlined, web-based tool for validating X-ray, neutron, and hybrid experimental data.
  • Validate model coordinates against structure factor data
  • Easily convert structure factor files between different formats mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, and more)
  • Check for and validate twinned or detwinned data

The latest release of SF-Tool includes support for neutron and hybrid experiments; incorporates checks from REFMAC1, PHENIX2, and SFCHECK;3 and
converts multiple data sets into a single mmCIF file.

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org.  

Contact deposit@deposit.rcsb.org with any questions about these resources.

1Refinement of Macromolecular Structures by the Maximum-Likelihood Method (1997) Murshudov, Vaguine, Dodson Acta Cryst. D53:240.
2PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Afonine, Bunk¯czi, et al. (2010) Acta Cryst. D66:213.
3SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structurefactor data and their agreement with the atomic model (1999) Vaguine, Richelle, Wodak Acta Cryst. D55:191.

31-Jul-2012

Protein Society Annual Symposium

Protein Society Annual Symposium.

Protein Society Annual Symposium.

RCSB PDB Director Helen Berman is the 2012 Awardee of the Carl Brändén Award of the Protein Society. The award, sponsored by the Rigaku Corporation, is given to an outstanding protein scientist who has also made exceptional contributions in the areas of education and/or service to the science.

This award recognizes her accomplishments toward enabling a freely available and uniform worldwide archive of 3D structural information for biomedical research and education.

The award will be conferred at the 26th Annual Symposium of The Protein Society (August 5-8, 2012) in San Diego, CA. Presentations by all of the 2012 awardees will take place during the afternoon Plenary Awards Session on Tuesday, August 7. Dr. Berman will present Trendspotting from the Protein Data Bank.

24-Jul-2012

Upcoming Meeting: ACA

Upcoming Meeting: ACA
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Visit booth 339 for demonstrations, new handouts, and more.

From July 28 - August 1, the RCSB PDB will be at the 2012 Meeting of the American Crystallographic Association in Boston, MA.

Stop by exhibition booth 339 to meet with members of the RCSB PDB and the PSI Structural Biology Knowledgebase (PSI SBKB) and pick up many new materials. Learn about new features such as RCSB PDB Mobile, Author Profiles, the wwPDB Common Tool for Deposition and Annotation, and much more.

Other meeting highlights will include:

  • Learn about How the PSI SBKB Can Enable Research from Maggie Gabanyi during the session on the Protein Structure Initiative: More Tools for the Home Lab (Sunday, Harbor III, 9:00 a.m.)
  • Get an update on The Worldwide Protein Data Bank: Current Projects during Monday's poster session (Presented by Jasmine Young, poster M-27).
  • In the Complementary Methods section, listen to Cathy Lawson describe the EMDataBank: Unified Data Resource for 3D Electron Microscopy (Tuesday, Harbor III, 9:30 a.m.)
  • During the Structure-Guided Drug Discovery session, learn about Data Management of Small Molecule Ligands, Antibiotics, and Peptide Inhibitors in the Protein Data Bank from RCSB PDB Director Helen Berman (Wednesday, Harbor III, 2:30 p.m.)

The RCSB PDB Poster Prize will be awarded to recognize a student poster presentation involving macromolecular crystallography.

17-Jul-2012

Different Ways To Explore New Entries

The Latest Structures widget, located on the home page, cycles through newly released entries.
(Click image to enlarge)
The Latest Structures widget, located on the home page, cycles through newly released entries.

On average, the wwPDB releases 170 structures into the PDB archive each week. The RCSB PDB offers different ways of exploring these new entries:

  • The Latest Structures widget on the home page provides a slideshow of individual entries. It displays the entry title, image, citation, and a link to the PubMed abstract, if available. Users can pause the show at any point to read the entire abstract, click on the entry title to view the entry's Structure Summary page, or go straight to the Jmol view of the entry.
  • The set of recently released structures can be launched in the Query Results Browser by clicking on the date listed at the top of the page and the link provided in the New Structures widget on the home page. From the Query Result Browser, users can drill through by category (organism, taxonomy, experimental method, and more), generate reports, and download structure and sequences files.
  • The MyPDB service can be set to run saved searches with each update. Email alerts (weekly or monthly) will be sent when new entries matching the search are released in the PDB archive.

10-Jul-2012

ISMB and 3DSIG Meetings

ISMB 2012.

This year, the International Society for Computational Biology is celebrating the 20th year of the ISMB - Intelligent Systems for Molecular Biology - conference (July 15-17. Long Beach, CA).

Presentations will include Internal pseudo-symmetry in proteins (Andreas Prlić) and Efficient searching and mining of the RCSB Protein Data Bank (Peter Rose).

At the ISMB Special Interest Group meeting Bioinformatics Open Source Conference (BOSC), Andreas Prlić will also present How to use BioJava to calculate one billion protein structure alignments at the RCSB PDB website.

At the 3Dsig: Structural Bioinformatics & Computational Biophysics satellite meeting, John Westbrook will discuss Format d¯j¯ vu: PDBx/mmCIF, the new data format for the wwPDB. Molecule of the Month author David Goodsell will describe Communicating and Interacting with the Molecular Cell (along with Arthur Olson).

Associate Director Phil Bourne is one of the 3Dsig Program Chairs.

Also at ISMB, the RCSB PDB Poster Prize will be awarded at ISMB for the best student poster presentation in the category of Structure and Function Prediction.

10-Jul-2012

Summer Newsletter Published

Summer Newsletter Published.

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Summer Newsletter Published

The summer 2012 issue (HTML | PDF) has been published.

The cover describes some of the new features added in the latest website release.

Deposition articles include how to deposit structures with ligands, and how the Journal of Biological Chemistry will require PDB validation reports by the end of the summer.

Features related to Data Query, Reporting, and Access describe how to use drill-down pie charts to browse the PDB, domain-based structural alignments, and customizing the home page to enable sequence searching.

The Outreach and Education section looks at the many options available for learning about the Molecule of the Month, the new Virus Structures poster, and meeting and event news.

The Education Corner, by Andrew K. Vershon, looks at how students are Learning Science by Doing Science at the Waksman Student Scholars Program.

This quarterly newsletter is published online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

03-Jul-2012

Author Profiles: Timeline Display of a Researcher's Structures

Author Profiles provide a timeline display of a researcher's structures.

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Author Profiles provide a timeline display of a researcher's structures.

Author Profiles display a vertical timeline of the structures that list a particular researcher as a Deposition Author or Primary Citation Author. To jump to a specific time period, select a year from the right navigation menu or scroll down the page to load subsequent years.

Find author profiles by entering the last name into the search box, and clicking a result.

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Find author profiles by entering the last name into the search box, and clicking a result.

The structures shown are ordered by deposition date and can be sorted to display either the newest or the oldest structures first. Images are linked to the Structure Summary page for the entry.

The first instance of a protein or protein complex is displayed in larger font than subsequent examples of similar molecules.

To access this feature, select the link from the left hand RCSB PDB menu, or from the PDB-101 Features pull-down menu.

For individual profiles, type an author's last name into the search box of the Author Profiles page and click one of the available results. Author Profile URLs are permanent links that can be copied and shared. 

For an example, visit J. Deisenhofer's Author Profile.

26-Jun-2012

Latest Website Release

Access the free download of RCSB PDB Mobile from Apple's App Store.
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Access the free download of RCSB PDB Mobile from Apple's App Store.

New and enhanced features have been added to the RCSB PDB, including:

  • RCSB PDB Mobile. Search the entire PDB, view the latest weekly release of structures, access your MyPDB account, view the entire catalog of Molecule of the Month articles, and more using either a WiFi or cellular data connection. RCSB PDB Mobile is an update of the beta-tested PDBMobile.
  • Author Profiles. This new PDB-101 feature displays a vertical timeline of the structures that list a particular researcher as a Deposition Author or Primary Citation Author. To jump to a specific time period, select a year from the right navigation menu or scroll down the page to load subsequent years.
  • Query and Display Features. Quickly search by Experimental and/or Molecule Type; view details about any revisions made to an entry from the Structure Summary page; and access Other Search Suggestions from top bar queries.

The What's New page has complete descriptions of all new features.

19-Jun-2012

Personalize the RCSB PDB with MyPDB

Users can tag structures to add them to a MyPDB bookmark list of entries, and add personal text annotations.
Users can tag structures to add them to a MyPDB bookmark list of entries, and add personal text annotations.
MyPDB can be accessed from the left-hand menu.
MyPDB can be accessed from the left-hand menu.

Notification of new structures that match stored queries can be emailed weekly or monthly.
Notification of new structures that match stored queries can be emailed weekly or monthly.

Create a personalized version of the RCSB PDB website with MyPDB.

  • Save searches online. The MyPDB Saved Query Manager stores any type of RCSB PDB structure search-a particular keyword, sequence, ligand, Advanced Search composite query, and more. Run these searches at any time with the click of a button.

  • Sign up for regular email alerts. Searches saved in MyPDB can be set to run with each update. Email alerts (weekly or monthly) will be sent when new entries matching the search are released in the PDB archive.

  • Store personal notes and bookmark structures. Save personal annotations and notes on the Structure Summary tab of any PDB entry. Want to keep a running list of interesting structures? MyPDB can keep a favorites list of PDB entries. The Personal Annotations summary page provides easy access to all of these tagged structures and annotations.

All MyPDB account information is kept private and secure, and can be updated at any time. Users can tag structures to add them to a MyPDB bookmark list of entries, and add personal text annotations.

For more information, a MyPDB flyer is available online (PDF).


19-Jun-2012

National Protein Modeling Champions

winning team

winning team

The National Science Olympiad Tournament was held May 18-19 at the University of Central Florida.

Teams built a model of MHC 1hsa, and brought along their prebuilt models of caspase protein 1i3o.

The top scoring teams in this event were:

  1. New Trier High School (IL)
  2. Troy High School (CA)
  3. Camas High School (WA)

Protein modeling is managed by the MSOE Center for BioMolecular Modeling and hosted in NJ by the RCSB PDB. This event will be on hiatus from the tournament for two years as other events are incorporated. The RCSB PDB's related twitter feed @buildmodels will continue to post education and PDB-related news and links.


12-Jun-2012

Top Bar SMILES String Searching

Use SMILES strings to search for ligands.

Use SMILES strings to search for ligands.

Typing a SMILES string (which encodes a chemical structure) in the top-bar search provides auto-completion options for a chemical search.

For example, typing the SMILES string Clc1ccccc1 (chlorobenzene) into the top-bar search provides the user with options to perform substructure, exact structure, or similar structure searches.

Selecting the exact structure search option redirects the user to the Ligand Summary for 8CL, which is the wwPDB Chemical Component Dictionary code for chlorobenzene.  Ligand Summary pages contain an overview of the chemical component, 2D and 3D images, links to other resources, and links to related ligands and PDB entries.

The top bar can also be used to search by ligand name or ligand ID.

In addition, the Chemical Component Search can be accessed by selecting the top bar ligand icon and clicking on [ additional ligand options ]. Launch the chemical structure editor to draw a structure or paste in a SMILES or SMARTS string to perform a substructure, exact, similarity, or superstructure search. Using this form, search for ligands by name, identifier, formula, and molecular weight.

Advanced Search supports the searches mentioned above, plus additional searches by chemical component type, binding affinity, sub-component, and more. These types of searches can be combined and even amended with searches for the associated structures.

05-Jun-2012

Molecule of the Month reaches 150

Click to view a slideshow of selected Molecule of the Month features.

Click to view a slideshow of selected Molecule of the Month features.

This month's article on Sliding Clamps is the 150th Molecule of the Month installment. With descriptions of molecules from AAA+ proteases to zinc fingers, Molecule of the Month provides an easy introduction to macromolecular structures and the PDB archive. View a slideshow for some other Molecule of the Month milestones by clicking on the image on the right.

Written and illustrated since January 2000 by David S. Goodsell (The Scripps Research Institute), each entry links to high resolution illustrations, suggests topics for further exploration, and hosts customized, interactive 3D molecular views. Specific structures are highlighted each month in the article, and shown in specific PDB-101 views (such as this example of a sliding clamp attached to flap endonuclease 1 (PDB 1ul1)).

As the keystone of the PDB-101 educational resource, the Molecule of the Month supports teachers and students at all levels in their exploration of biology at a structural level.

PDB-101 supports different ways of exploring the Molecule of the Month, including:

Molecule of the Month articles are available from the main RCSB PDB home page, top bar searches, structure search results, and Structure Summary pages.

Have suggestions for future Molecule of the Month columns? Let us know!

Related Resources

29-May-2012

Tour the PDB with Drill-down Pie Charts

Users can tour the PDB archive by `drilling down` on significant properties of structures such as Organism and Polymer Type with just a few clicks. This example shows the path to the EC distribution of structures from humans. Clicking on any link returns the structures that match all selected parameters. This feature is available to navigate through all search results and for the entire PDB archive.
(Click image to enlarge)
Users can tour the PDB archive by "drilling down" on significant properties of structures such as Organism and Polymer Type with just a few clicks. This example shows the path to the EC distribution of structures from humans. Clicking on any link returns the structures that match all selected parameters. This feature is available to navigate through all search results and for the entire PDB archive.

Standard characteristics of PDB entries--resolution, release date, experimental method, polymer type, organism, taxonomy--are used to create searchable data distribution summaries.

The Explore Archive widget on the home page provides a quick statistical overview of the PDB. Browse the charts individually, or view them all together by clicking on the "Show all" link. Clicking on a pie chart image will display a more detailed graphic that lists the percentages for the categories shown.  Selecting one of the listed results will launch the corresponding structures in the Query Results Browser.

Data Distributions also appear at the top of the Query Results Browser, and can be used to view a quick statistical overview and to refine the results into subsets of interest. For example, users can drill-down these faceted search options to quickly access high resolution entries from a structure type search; human-related entries from a sequence search; or most recent entries returned from a chemical component search for a particular ligand. Any combination of categories is possible.  

These charts can be hidden from the query results for users who want to only view the individual entries.

Data distribution summaries can also be used to explore the latest weekly update of PDB entries.

22-May-2012

Domain-based Structural Alignments

The sequence diagram for PDB ID 3BMV shows the corresponding UniProtKB sequence, the SEQRES and ATOM records, and the various annotations that are available.

(Click image to enlarge)
The sequence diagram for PDB ID 3BMV shows the corresponding UniProtKB sequence, the SEQRES and ATOM records, and the various annotations that are available.

Access pre-calculated systematic structure comparisons for all proteins from a Structure Summary's 3D Similarity tab.

In the example of the 3D Similarity tab for 3BMV, selecting

(Click image to enlarge)
In the example of the 3D Similarity tab for 3BMV, selecting "view" for the 7th ranked domain PDP:3DHUAa launches the structure alignment view for the alpha amylase domains of 3BMV and 3DHU.  Selecting the link for PDP:3DHUAa under the column Domain 2 returns the 3D Similarity tab for entry 3DHU.

To provide more accurate results, the latest version of the 3D Similarity tab uses domain-based protein structure alignments instead of chain-based alignments.

For an example, see the 3D Similarity tab for glucanotransferase (PDB ID 3BMV).

An image of the sequence highlights how the residues listed in the sequence (SEQRES) and in the atom records (ATOM) map onto the relevant parts of the UniProtKB sequence, along with annotations from DSSP, SCOP, PDP and Pfam.

Domains are also highlighted in a table that displays the most important calculated results and scores. Domains can be selected from the pull down menu above the table, or by clicking on a domain in the sequence image.

The table can be sorted and filtered, and offers links to a 3D structure alignment in Jmol (from the results column) and to information about similar domains. In the example of the 3D Similarity tab for 3BMV, selecting "view" for the 7th ranked domain PDP:3DHUAa launches the structure alignment view for the alpha amylase domains of 3BMV and 3DHU.  Selecting the link for PDP:3DHUAa under the column Domain 2 returns the 3D Similarity tab for entry 3DHU.

The calculation of the domain-split representative is an extension of our sequence clustering approach. To remove redundancy, we start with a 40% sequence identity clustering procedure, and select a representative chain from each sequence cluster. If the representative chain contains multiple domains, each is included. SCOP 1.75 domain assignments are used when available. Otherwise, the assignments are computed using ProteinDomainParser.

15-May-2012

New Poster: Virus Structures

New Poster: Virus Structures.
New Poster: Virus Structures.

Learn about polyhedral, helical, complex, and enveloped viruses with examples drawn at approximately 900,000x magnification with a new poster that focuses on the shapes and sizes of different virus structures.

Structures from the feline distemper virus to mimivirus are highlighted.

This Virus Structures (PDF) flyer joins other posters that illustrate The Structural Biology of HIV, How Do Drugs Work, Molecular Machinery, the Ribosome, and Toll-like Receptors. Download them all from PDB-101.

PDB-101 also offers virus-related lesson plans and a template to fold a model of the dengue virus.

Virus Structures was created by the RCSB PDB and the EMDataBank.

08-May-2012

Bookmark and Post Webpages

'Share this Page' button.
(Click image to enlarge)
'Share this Page' button.

Users can easily send and store RCSB PDB web pages using the "Share this Page" button.

With this service, favorite PDB entries, Molecule of the Month articles, and other features can be easily emailed to colleagues or posted to Facebook, Twitter, and LinkedIn.

08-May-2012

Customized Home Page: Sequence Search

The Search Sequence widget can be added to the home page.  All widgets with a dark blue bar on top can be moved around on the page by dragging the arrow buttons.
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The Search Sequence widget can be added to the home page.  All widgets with a dark blue bar on top can be moved around on the page by dragging the arrow buttons.

The RCSB PDB homepage is comprised of web widgets that can be moved around, minimized, or hidden so users can create a website that reflects their interests. Frequently-used features can be moved to the top, while less popular items can be hidden or collapsed.

Enter a PDB ID to select a chain.
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Enter a PDB ID to select a chain.

The Sequence Search widget can search for a given sequence or a particular chain of any PDB entry using BLAST, FASTA, or PSI-BLAST. Options include specifying the E cut-off value and filtering low complexity.

To add this widget to your home page, select the Customize This Page button from the left menu.  Download Files, Structure Comparison, and ADIT Deposition widgets can also be added.

01-May-2012

Latest Website Release

Sequence diagram for PDB ID 3BMV. It shows the corresponding UniProt sequence, the SEQRES and ATOM records as well as various annotations that are available.
(Click image to enlarge)
Sequence diagram for PDB ID 3BMV. It shows the corresponding UniProt sequence, the SEQRES and ATOM records as well as various annotations that are available.

New and enhanced features have been added to the RCSB PDB website, including:

* Domain-based Structural Alignments. The 3D Similarity tab provides pre-calculated systematic structure comparisons for all PDB proteins. The new version of this feature provides domain-based protein structure alignments instead of chain-based alignments.

* Improved Search Options. New features include the highlighting of search terms in the results list; SMILES string search options enabled from the top bar; an Advanced Search option to search LINK records to find structures containing interresidue connectivity; and improved mapping between UniProtKB ID and EC number.

* Enhanced Ligand Summary Reports. Ligand Summary Reports include information about selected ligands such as formula, molecular weight, name, SMILES string, which PDB entries are related to the ligand, and how they are related. For each ligand included in the report, a sub-table can be selected to show lists of all related PDB entries that contain the ligand, the entries that contain the ligand as a free ligand, and entries that contain the ligand as part of a larger, polymeric ligand.

To generate a report, select the Ligand Hits tab followed by the summary report option from the Generate Reports pull-down menu.

The What's New page has complete descriptions of all new features.

24-Apr-2012

Rutgers Day (April 28)

Rutgers Day.
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Rutgers Day 2012.

Rutgers Day is a full day of discovery and lively activities that showcase the varied resources, departments, and people at the university.  The RCSB PDB will be part of the Department of Chemistry and Chemical Biology's exposition on Busch Campus. Visitors will be able to build 3D DNA and virus structure models next to experiments and demonstrations of how chemistry impacts our lives.

Rutgers Day will take place from 10 a.m. - 4 p.m. rain or shine. Admission and parking are both free.

24-Apr-2012

Create a Collage of Structures

The Generate Reports pull-down menu can be used to create an image collage.
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The Generate Reports pull-down menu can be used to create an image collage.

Different types of reports can be generated for a set of PDB entries, including the option to generate a collage of molecular images.

To create a collage, search for a group of structures, pull down the Generate Reports menu and select Custom Report>Image Collage.  The query results will appear as a series of tiled molecular pictures.

Image collage of virus structures.
(Click image to enlarge)
Image collage of virus structures.

Mousing over each image in the collage displays the structure title; clicking on the small image shows a larger version. The PDB ID listed links to the corresponding Structure Summary page.

Image collages can be customized by the size of the images displayed and how many images are shown per page.

Other Generate Reports options include creating customized tables or viewing pre-generated summary reports about structure, sequence, ligand, Structural Genomics Center, primary citation, and biological details.

17-Apr-2012

DNA Day 2012: April 20

Build a paper model of DNA using the activity found at PDB-101's Educational Resources.
(Click image to enlarge)
Build a paper model of DNA using the activity found at PDB-101's Educational Resources.
Structure of B-DNA dodecamer 1bna.
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Structure of B-DNA dodecamer 1bna.

NHGRI's National DNA Day commemorates the completion of the Human Genome Project and the discovery of DNA's double helix. It's also a day for students, teachers, and the public to learn more about genetics and genomics.

Celebrate by:

17-Apr-2012

Exhibiting at Experimental Biology

Experimental Biology 2012.

The RCSB PDB will be exhibiting along with the PSI SBKB at the American Society for Biochemistry and Molecular Biology's Annual Meeting (April 21-25, San Diego, CA), which is held in conjunction with the Experimental Biology conference. Stop by booth #447 to meet with RCSB PDB staff, explore new website features, and to pick up RCSB PDB materials such as the How Do Drugs Work? poster.

10-Apr-2012

Spring Newsletter Published

Cover of the Spring 2012 Newsletter.

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Cover of the Spring 2012 Newsletter.

The spring 2012 issue (HTML | PDF) has been published.

The cover feature looks at a special animation that highlights the replisome.

Deposition articles describe how to volunteer structures for study by Foldit gamers, how to deposit structures with ligands, 2011 deposition statistics, and the Electron Microscopy Validation Task Force meeting report.

Features relating to "data out" introduce readers to the New Structures Widget, Ligand Summary Pages, how to browse the PDB by GO Terms, EC Number, Source Organism, and more, and using Protein Workshop to visualize molecular surfaces.

The Outreach and Education section describes the RCSB PDB's activities at the San Diego Festival of Science and Engineering, PDB-101 resources, protein modeling at the Science Olympiad, updated RCSB PDB training materials, and more.

The Education Corner, by Hazel M. Holden and Dan Toomey, describes their program with middle school students called Project CRYSTAL: Crystallographers Researching with Young Scientists, Teaching and Learning.

This quarterly newsletter is published  online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

03-Apr-2012

Depositing Structures with Ligands

Ligand Expo can also be used to check and confirm the chemistry of a chemical component.  Shown is the correct sterochemistry for alpha-D-mannose (on the left, ID: MAN) and for N-acetyl-D-glucosamine  (on the right, ID: NAG).

(Click image to enlarge)
Ligand Expo can also be used to check and confirm the chemistry of a chemical component. Shown is the correct sterochemistry for alpha-D-mannose (on the left, ID: MAN) and for N-acetyl-D-glucosamine (on the right, ID: NAG).

Ligand Expo (ligand-expo.rcsb.org) accesses chemical and structural information about all small molecule components found in PDB entries. It is based upon the Chemical Component Dictionary maintained by the wwPDB. When depositing a structure with a ligand

  • Search Ligand Expo for a chemical component that matches your ligand
  • If a match is found, use the corresponding three-character code for the ligand in your coordinates
  • If the ligand is new, choose a new three-character code for the ligand
  • When depositing your structure with ADIT, upload the chemical name and formula and/or a file showing the chemical image for the new ligand into the Ligand Information section

Ligand Expo can search the Chemical Component Dictionary using uploaded data files (e.g., PDB, MOL/SDF, Refmac/Phenix monomer library (mmCIF)); chemical name; formula; SMILES string; and ID code.

Searches for instances of ligands associated with macromolecular structures can also be performed at www.pdb.org using a variety of options, including the top bar Chemical Name/ID search, Advanced Search, and the Chemical Structure Search. Users can then explore the ligand structures and the related PDB entries. Online screencasts are available at the RCSB PDB site to help users explore these features.

27-Mar-2012

Browse the PDB by GO Terms, EC Number, Source Organism, and More

blank image.
Browse icon.

RCSB PDB's Browse Database feature explores the PDB archive using different hierarchical trees. Browsers are available to search for related terms and structures based upon the following classifications:

Click Browse from the top of every RCSB PDB page to access this feature, and then the desired Browser Tab to start searching.

20-Mar-2012

Visit the San Diego Festival of Science and Engineering on March 24

blank image.

On Saturday March 24, visitors to the RCSB PDB booth at the San Diego Festival of Science and Engineering's EXPO DAY will learn about the basic building blocks of life by building 3D models of DNA and small proteins. They can also watch animations of 3D proteins and nucleic acids, and take home posters and other materials about these fascinating structures.

EXPO DAY is the grand-slam-science-finale to a week of big events at San Diego State University, Balboa Park and California State University San Marcos. Activities include building what could be the world's longest DNA model, which will be presented at the main stage at EXPO DAY.

Over 20,000 kids, families, scientists, engineers, educators, and other community members are expected to take part in this year's EXPO DAY, a free-to-the-community event! Visit www.sdsciencefestival.com for complete details.

Can't make it to San Diego? Build models of DNA and the dengue virus at home using these PDFs from the Educational Resources page.

20-Mar-2012

J.P. Stevens HS Wins NJ Protein Modeling Event

Protein modeling state champions from J.P. Stevens High School (Edison).e
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Protein modeling state champions from J.P. Stevens High School (Edison).
The RCSB PDB judges provided feedback to the students.
(Click image to enlarge)
The RCSB PDB judges provided feedback to the students.

26 teams from high schools in New Jersey demonstrated their understanding of protein structure at the March 13 State Science Olympiad competition. Teams had previously scored well at one of the three regional competitions that took place in January.

Jmol was used to build models onsite.
(Click image to enlarge)
Jmol was used to build models onsite.

The focus of this year's event uses the example of the discovery and treatment of a rare genetic trait to explore proteins involved in the regulation of apoptosis. Related Molecule of the Month columns and Jmol are key resources for this event. Related information is also posted on twitter.com/#!/buildmodels. For an overview, see education.pdb.org and cbm.msoe.edu/stupro/so/index.html.

Teams submitted hand-built 3D models of caspase (PDB ID 1i3o) on the morning of the event. The models represented the protein backbone, with additional points awarded for structures with details that highlighted important parts of the structure.

During the event itself, the students quickly built a model of PARP (PDB ID 3od8) and answered questions on a written exam.

RCSB PDB team members judged this competition, and met with teams at the end of the day to discuss results.

Congratulations to all participating teams--there were many great models, abstracts, and responses to the written exam.

Top Protein Modeling Results

  1. JP Stevens (85.25)
  2. Princeton (84.75)
  3. East Brunswick (82.5)
  4. West Windsor Plainsboro South (82.25)
  5. Hillsborough (79.25)
  6. Livingston (74.5) 

The full results are available at education.pdb.org.

Special thanks to our judges from the RCSB PDB (Luigi Di Costanzo, Brian Hudson, and event organizer Christine Zardecki), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to buildmodels@deposit.rcsb.org.

For protein-related tips and news of interest to students and educators, follow us on twitter@buildmodels.

13-Mar-2012

Sound Science

Nucleosomes as shown in Hollow. Image courtesy of Drew Berry.
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Nucleosomes as shown in Hollow. Image courtesy of Drew Berry.

Biomedical animator Drew Berry (Walter and Eliza Hall Institute of Medical Research) is known for his fantastic and detailed depictions of complex biomolecular systems. His award-winning work, which can be viewed online, in television and film, and in museums throughout the world, now appears in new and unusual venues thanks to a collaboration with the musician Bjork.

Bjork's latest project Biophilia manifests her love for music, technology, and nature in many ways: an album, iPad app, touring production (which includes a 24-woman Icelandic choir and a musical Tesla coil), and a music education initiative.

To accompany the song Hollow, Bjork's meditation on biological ancestry, Berry created a lush landscape for DNA to replicate (and sparkle) to the music. Molecular machines work at realtime speed, culminating in the appearance of Bjork as a complex protein structure. Many of the molecular shapes, illustrated with great depth and rich color, were created with the help of crystal structure data from the PDB.

Recently released online at NPR, the animation is projected on screens throughout the venues hosting Bjork's concerts, and is highlighted on stage during the performance of Hollow. The related iPad app includes the Hollow movie and a 'machine' that lets where users can queue up floating enzymes to interact with the replisome to create music.

13-Mar-2012

Preview New 3D Similarity Tab

The 3D Similarity tab provides pre-calculated systematic structure comparisons for all PDB proteins. A new version of this feature, available this spring, will be based on domain-split alignments. The new 3D Similarity tab can be previewed at beta.rcsb.org. For an example, see the 3D Similarity tab for PDB entry 3BMV.

When this feature is released to the production site, whole chain comparisons will be discontinued from the 3D Similarity tab.

The Comparison Tool will continue to support whole protein chains comparisons, in addition to domain comparisons.

13-Mar-2012

PDBMobile and iOS 5.1

Changes made in the latest iPhone operating system will break existing installations of PDBMobile.  iPhone users running the new iOS 5.1 should delete and then reinstall PDBMobile. Fresh PDBMobile installations will work on iOS 5.1, or any of the previous iOS versions above version 4.

A new and improved version of PDBMobile will be available in the app store this spring.

More information about PDBMobile is available in the FAQ.

06-Mar-2012

Explore a Structural View of Biology at PDB-101

Biological Energy category.
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Biological Energy category.

PDB-101's Structural View of Biology promotes a top-down exploration of the PDB.

To start, select from high-level categories describing function: Protein Synthesis, Enzymes, Health and Disease, Biological Energy, Infrastructure and Communication, Biotechnology and Nanotechnology.  

The Biological Energy category, for example, involves PDB structures that reveal how cells use chemical energy, light energy, electrical energy and mechanical energy to power the processes of life. The structures are organzied into the following subcategories:

  • Capturing the Energy in Food
  • Photosynthesis
  • Molecular Motors
  • Creating and Capturing Light

These subcategories link to Molecule of the Month features related to the topic.  Capturing the Energy in Food includes articles about structures such as pepsin (an enzyme that digests proteins), lactate dehydrogenase (creates lactic acid as part of anaerobic respiration), and glycolytic enzymes (used to break down glucose).

Each article then links to special PDB-101 Structure Focus pages that highlight specific entries discussed in the article. These pages describe why the particular structure has been selected as an example, along with an interactive 3D view, sequence display, ligand information, and links to other structures examples discussed in the Molecule of the Month article. For example, the feature on glycolytic enzymes links to Structure Focus pages for all enzymes involved in glycolysis. These Focus pages are streamlined versions of the more complex Structure Summary pages available for all PDB entries.

The Structural View of Biology is a major part of PDB-101, the RCSB PDB resource that packages together materials and tools that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public. Click on the blackboard logo from the top of any RCSB PDB page to enter.

Other areas in PDB-101 include indexes of all Molecule of the Month articles; Educational Resources, with related tools, posters, tutorials, activities, lesson plans, and more; and the Understanding PDB Data reference for exploring and interpreting PDB data.

28-Feb-2012

Visualize Molecular Surfaces with Protein Workshop

The visibility and surface color of selected chains can be adjusted using Protein Workshop.
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The visibility and surface color of selected chains can be adjusted using Protein Workshop.

The molecular graphics program Protein Workshop1 can be used to generate molecular surfaces to aid in the display of quaternary structure, protein-protein interactions, and binding sites.  This robust feature is able to handle very large assemblies, such as virus capsids.

Surfaces are created for all macromolecule chains in a PDB entry using an algorithm from D. Xu and Y. Zhang.2

A detailed description for using this feature includes: how to create molecular surfaces; color by surface, chain, and entity; make a specific surface transparent; and tips.

Protein Workshop can be launched from on every Structure Summary page. A link is located underneath the image of the biomacromolecule.

The program can also be used to generate high resolution images for publication.

Shown: PDB ID 1e79 The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution.  C. Gibbons, M.G. Montgomery, A.G.W. Leslie, J.E. Walker (2000) Nat.Struct.Biol. 7: 1055

  1. 1. J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications BMC Bioinformatics 6:21.
  2. 2. D. Xu and Y. Zhang. (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4: e8140.

21-Feb-2012

Visit the Biomolecular Discovery Dome at Biophysical Society

Biophysical Society meeting.

See proteins and molecular machines like you never have before in the Biomolecular Discovery Dome, an audio-visual immersion experience that takes you inside the world of cells and viruses.

The Biomolecular Discovery Dome will be located near the registration area at the Biophysical Society meeting on Sunday, February 26 and Monday, February 27 in San Diego, CA.

Short films scheduled to appear will highlight:

  • Viruses, narration and gallery visualization of viruses (National Center for Macromolecular Imaging (NCMI))
  • Trypanosome Brucei and African sleeping sickness (NCMI)
  • Ribosomes (NCMI)
  • Crystallographic Point Groups (a musical tribute to the 100th anniversary of X-ray diffraction, NCMI)
  • Exploring the Cell (Istituto di Fisiologia Clinica-Consiglio Nazionaledell Ricerche, Italy)
  • Drug Discovery & HIV (University of California, San Francisco)

This Biomolecular Discovery Dome is sponsored by the Biophysical Society's Public Affairs Committee.


21-Feb-2012

New Structures Widget

The New Structures widget.
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The New Structures widget..

Available from the home page, the New Structures widget links to the latest structure released, the structure papers related to this release, and to the Unreleased Entry Search.

  • Latest Release: The weekly update of new PDB entries can be explored and refined using the query results viewer.
  • New Structure Papers: A clickable list of citations associated with the entries in the latest PDB release
  • Unreleased Entries: Find structures that are being processed or on hold waiting for release. Data can be searched by PDB ID, author, title, status, sequence availability (some sequences are released in advance of the coordinates), and structural genomics project or center name.

The appearance of widgets on the RCSB PDB home page can be customized.  For more, see the Winter 2012 Newsletter.

14-Feb-2012

Ligand Summary Pages

Ligand Summary page for CFF (caffeine).

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Ligand Summary page for CFF (caffeine).

Ligand Summary Pages provide information for all of the entries found in the wwPDB's Chemical Component Dictionary.

Similar to Structure Summary pages for PDB entries, Ligand Summary Pages are organized into widgets that highlight different types of information. 

For example, view the Ligand Summary Page for caffeine (Ligand ID CFF) to access:

  • Chemical Component Summary: an overview of the structure, including name, identifiers, synonyms, and SMILES and InCHI information
  • Related PDB Entries: searches for other structures where the ligand appears as a free ligand
  • Related Ligands: links to Summary Pages for similar ligands and stereoisomers, and automatically enters the ligand in the Chemical Structure Search tool to build related ligand searches
  • Ligand Image: toggles between a static image and a 3D Jmol view
  • Links: connects to information about the chemical component at external resources (BindingDB, HIC-Up, PDBeChem and more) and the RCSB PDB's Ligand Expo

These summaries can be accessed by performing a ligand search, selecting a ligand from a PDB entry's Structure Summary page, and from the Ligand Hits tab for query results.

07-Feb-2012

Volunteer Structures For Foldit

Foldit logo.e
Foldit logo.
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(Click image to enlarge)
Submitting a structure for Foldit use.

Foldit is an online game that attempts to predict the structure of a protein by taking advantage of humans' puzzle-solving intuitions and having people play competitively to fold the best proteins.  Gamers use the Foldit interface to build protein models based upon the amino acid sequence.

ADIT depositors can submit their sequences to serve as puzzle challenges for the Foldit community.  When submitting an entry to the PDB, select the following options in the Release Status category:

  •  Release status for coordinates: Hold for 8 weeks
  •  Prerelease status for sequence information: Release Now
  •  CASP/CASD/other method development target: Foldit

The deposition will appear as a Foldit Target in the Unreleased Structures search. Foldit will use the prereleased sequence as a puzzle, and gamers will be able to compare their predicted models to the experimental data when it is released 8 weeks later.

07-Feb-2012

Free Webinar and Updated Tutorial

Screenshot of Summary Page tutorial.
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Screenshot of Summary Page tutorial.
Screenshot of Advanced Search tutorial.
(Click image to enlarge)
Screenshot of Advanced Search tutorial.
Screenshot of Ligand Explorer tutorial.
(Click image to enlarge)
Screenshot of Ligand Explorer tutorial.

OpenHelix, the provider of training on hundreds of free, publicly accessible bioinformatics and genomics resources, will provide a free webinar: Introduction to RCSB PDB on Wednesday, February 15th, at 11 a.m. PT/2:00 p.m. ET/18:00 UTC/GMT.

In the webinar, you'll learn how to use the features and functions needed to start using RCSB PDB effectively, including:

  •  searching for structures and related information using a variety of strategies
  •  understanding the results and structure summary pages and link to additional information
  •  visualizing structures
  •  customizing search results and website display

Register at www.openhelix.com/cgi/webinars.cgi.

OpenHelix has also updated their free, online training materials to reflect many new RCSB PDB features, including the top bar searching feature with category options, auto-complete feature, improved macromolecule name queries, and PDB-101.

In addition to a narrated tutorial, the animated PowerPoint slides used as a basis for the tutorial, handouts, and exercises are also available for download. This can save a tremendous amount time and effort for teachers and professors to create classroom content.  These files can be downloaded from www.openhelix.com/pdb.

31-Jan-2012

Announcement: Meeting on Hybrid Methods

Meeting Flyer
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Meeting Flyer
Dynein cargo trasnport by Graham Johnson
Dynein cargo transport by Graham Johnson

The 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held March 14-18, 2012 in Lake Tahoe, CA.

The overall goal is to illustrate the power of combining state of the art methods to tackle important and challenging biological problems and to identify limitations and gaps in currently practiced hybrid methods. The central premise is that gaining a comprehensive understanding of the highly sophisticated complexes, machines, and organelles of the cell requires the coordinated application of complementary biophysical approaches (hybrid methods).

An outstanding panel of speakers has been assembled, including keynote presentations by Wesley I. Sundquist (University of Utah) and Susan Taylor (UC San Diego) and a "vision" talk by Michael Rossmann (Purdue University).

31-Jan-2012

Free Webinar on How to use the RCSB PDB

OpenHelix, the provider of training on hundreds of free, publicly accessible bioinformatics and genomics resources, will provide a free webinar: Introduction to RCSB PDB on Wednesday, February 15th, at 11 a.m. PT/2:00 p.m. ET/18:00 UTC/GMT.

In the webinar, you'll learn how to use the features and functions needed to start using RCSB PDB effectively, including:

  • how to search for structures and related information using a variety of strategies
  • to understand the results and structure summary pages and link to additional information
  • how to visualize and manipulate the structures
  • to customize your results by using the many formatting options

Register at www.openhelix.com/cgi/webinars.cgi.

OpenHelix also offers a suite of tools for learning how to use the RCSB PDB (narrated tutorial, slides, and exercises).

24-Jan-2012

Newsletter Published

Winter 2012 Newsletter.
(Click image to enlarge)
Winter 2012 Newsletter.

The winter 2012 issue (HTML | PDF) highlights 2011 statistics for deposition and distribution, the latest wwPDB News, and quick searching at the RCSB PDB website.

In the Education Corner, the 2011 RCSB PDB Poster Prize awardees describe how they are Learning to Become a Structural Biologist.

The newsletter also describes the many ways users can search for ligands and for homo- and hetero-multimer structures, Molecule of the Month developments, and more.  

This quarterly newsletter is published  online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

17-Jan-2012

NJ Science Olympiad Protein Modeling Results

55 teams from high schools in New Jersey demonstrated their understanding of protein structure at three regional Science Olympiad competitions.

The focus of this year's event uses the example of the discovery and treatment of a rare genetic trait to explore proteins involved in the regulation of apoptosis. Related Molecule of the Month columns are key resources for this event. For an overview, see http://cbm.msoe.edu/stupro/so/index.html.

The top scoring NJ teams were:

South Brunswick (First place, south) with their prebuilt model of a caspase protein. (Click image to enlarge)South Brunswick (First place, south) with their prebuilt model of a caspase protein.

Teams quickly build models on site, and take a written exam. (Click image to enlarge)
Teams quickly build models on site, and take a written exam.
Luigi Di Costanzo describes how models were scored at the event. (Click image to enlarge)
Luigi Di Costanzo describes how models were scored at the event.
Southern (January 7)
  1. South Brunswick
  2. West Windsor Plainsboro North
  3. Moorestown Friends
  4. Cherry Hill EastMATES Academy
  5. 6 Cherry Hill West


Central (January 10)
  1. JP Stevens
  2. Hillsborough
  3. Princeton
  4. West Windsor Plainsboro North
  5. Summit
  6. New Providence


Northern (January 12)
  1. West Windsor Plainsboro #1
  2. West Windsor Plainsboro #2
  3. Bergen County Academies
  4. Al-Ghazaly HS
  5. JP Stevens
  6. Livingston


Full results will be posted, along with updates, pictures, and more at education.pdb.org and on Twitter at @buildmodels.

Protein modeling will be one of several events at Science Olympiads across the country. Teams are recognized for their performance in individual events and in the overall tournament.

The RCSB PDB will also be involved with protein modeling at the San Diego Science Olympiad tournament that will be held February 18, 2012.

Many thanks to the RCSB PDB judges (Luigi Di Costanzo, Sutapa Ghosh, Brian Hudson, Huangwang Yang, Christine Zardecki, and Marina Zhuravleva), the NJ Science Olympiad organizers and volunteers, the host colleges (Camden County, Union County, and NJIT), and to the MSOE Center for BioMolecular Modeling for the materials and design of this event.

We look forward to seeing everyone at the state finals in March!

10-Jan-2012

Web Services for Accessing PDB Data

Web Services can help software developers build tools that efficiently interact with PDB data. Instead of storing coordinate files and related data locally, Web Services let software tools access the RCSB PDB remotely. Detailed documentation for accessing these Web Services is available (RESTful | SOAP).

RESTful services exchange XML files in response to URL requests. RESTful search services return a list of IDs for Advanced Search and SMILES-based queries. RESTful fetch services return data when given IDs, including PDB entity descriptions, ligand information, third-party annotations for protein chains, and PDB to UniProtKB mappings. Web Services can also be used to generate pre-defined summary and customizable reports for query results. A new service for accessing pre-released sequences in FASTA format has been recently added.

Improvements are being made based on community feedback. Please let us know if there are website options that you think should be offered as a web service.

03-Jan-2012

Annual Report Published

Structures highlighted in the year's Molecule of the Month features are highlighted on the cover and throughout the report.
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Structures highlighted in the year's Molecule of the Month features are highlighted on the cover and throughout the report.

Download the 2011 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

Milestones covered include the ways in which searching has been simplified, and the features of the new PDB-101 educational resource. wwPDB efforts, such as the PDB40 anniversary celebration and the publication of the X-ray Validation Task Force's recommendation report, are also highlighted.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive.  This edition, the RCSB PDB's twelfth, is available as a PDF download  from www.rcsb.org/ar11. If you would like a printed copy, please send your postal address to info@rcsb.org.