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Year 2004 News

Contents:

28-Dec-2004 Happy Holidays from the RCSB PDB
28-Dec-2004 RCSB PDB Beta Site described in Nucleic Acids Research Database Issue
21-Dec-2004 PDB Focus: Ligand Depot--a Small Molecule Information Resource
14-Dec-2004 PDB Focus: Worldwide Data Annotation
07-Dec-2004 Open House at RCSB-Rutgers on Thursday, December 9, 2004
07-Dec-2004 RCSB Beta Site Focus: Using PubMed Abstracts
30-Nov-2004 RCSB PDB's 2004 Annual Report Now Available
23-Nov-2004 Publication of "PDBML: the representation of archival macromolecular structure data in XML"
23-Nov-2004 Oral History of PDB Archived with the Chemical Heritage Foundation
16-Nov-2004 RCSB PDB Exhibit at International Conference on Structural Genomics
16-Nov-2004 RCSB PDB's Art of Science Exhibit at Fairleigh Dickinson University
09-Nov-2004 New Data CD Release
09-Nov-2004 Cryo-EM Workshop held at RCSB-Rutgers
02-Nov-2004 RCSB Beta Site Focus: Searching the PDB based on NMR Experimental Details
26-Oct-2004 Fall Newsletter Published
19-Oct-2004 Design and Content of RCSB PDB Data Deposition Services Enhanced
12-Oct-2004 PDB_EXTRACT and data deposition tools described in Acta D paper
05-Oct-2004 RCSB Beta Site Focus: Database Browsers
28-Sep-2004 RCSB PDB Poster Prize - ECM Winner Announced
21-Sep-2004 RCSB PDB Art of Science Exhibit Part of EMBL-Hamburg's "Structural Biology at Crossroads: From Biological Molecules to Biological Systems"
14-Sep-2004 "The Impact of Structural Genomics on the Protein Data Bank" Published
07-Sep-2004 RCSB PDB Flyer: 5 Easy Steps for Crystal Structure Deposition
31-Aug-2004 Symposium: Database Challenges in Biology
24-Aug-2004 New Data CD Release
17-Aug-2004 PDB Focus: How are HPUB structures released?
10-Aug-2004 RCSB PDB at Protein Society Meeting
10-Aug-2004 Presentations from the ACA Workshop "A Protein Crystallographic Toolbox: CCP4 Software Suite and PDB Deposition Tools Available Online"
03-Aug-2004 ACA Report: Poster Prize Awarded; Presentations, Demonstrations, and Workshops
27-July-2004 Summer Newsletter Published
20-July-2004 RCSB PDB Presentations and Demonstrations at 3D SIG and ISMB/ECCB, July 29 - August 4, 2004 in Glasgow, Scotland
13-July-2004 RCSB PDB Poster Prize awarded at AsCA meeting
06-July-2004 Come visit us in "Data Alley" -- RCSB PDB Demonstrations, Poster Prize, Workshops, and More at the ACA Annual Meeting July 17-22 in Chicago, IL
29-June-2004 Links to the OCA Data Browser Available
22-June-2004 Batch File Download Script Now Available
15-June-2004 RCSB PDB Poster Prize to be Awarded at AsCA -- Instructions for Entering
15-June-2004 Legacy AutoDep Deposition System Closing at RCSB
8-June-2004 PDB_EXTRACT integrated into CCP4 Program Suite
1-June-2004 TargetDB and Ligand Depot papers published in Bioinformatics
25-May-2004 "The Protein Data Bank and lessons in data management" published in Briefings in Bioinformatics
25-May-2004 Structural Bioinformatics (3D SIG)
18-May-2004 Workshops at ACA Chicago Meeting
11-May-2004 FASTA Sequence Files on RCSB PDB FTP Archives
27-Apr-2004 RCSB PDB High School Workshop on Molecules in Chicago - July 18, 2004
27-Apr-2004 CD-ROM Subscriber Questionnaire Results Released
20-Apr-2004 RCSB PDB Newsletter 21 Released
13-Apr-2004 RCSB Poster Prize awarded at RECOMB
13-Apr-2004 RCSB PDB at the Experimental Nuclear Magnetic Resonance Conference (ENC)
06-Apr-2004 A new 'QuickSearch' feature is available
30-Mar-2004 RCSB PDB at RECOMB and National Science Teachers Association's National Convention
23-Mar-2004 PDB Focus: XML Data Files
16-Mar-2004 PDB Poster Prize, Demonstration at RECOMB 2004
09-Mar-2004 A new 'QuickSearch' feature is available on the Beta site
02-Mar-2004 Molecular Machinery Poster Available as PDF
24-Feb-2004 New CD-ROM Release
17-Feb-2004 Release of ADIT-NMR Deposition Tool at BMRB
10-Feb-2004 "The PDB: A case study in management of community data" published in Current Proteomics
03-Feb-2004 "Validation of protein structures for the PDB" paper published in Methods in Enzymology
03-Feb-2004 PDB Art of Science Exhibit Visits the University of Wisconsin-Madison
27-Jan-2004 Protein Data Bank Opens New Era With Broader Support
20-Jan-2004 RCSB PDB Newsletter 20 Released
20-Jan-2004 PDB Chemical Component Dictionary Format Description Available
13-Jan-2004 Molecule of the Month Highlighted in BAMBED
06-Jan-2004 PDB Focus: Accessing and Understanding Biological Units

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


28-December-2004

Happy Holidays from the RCSB PDB

The RCSB PDB staff wish to extend our best wishes to the community for a happy holiday season and a wonderful new year!

28-December-2004

RCSB PDB Beta Site described in Nucleic Acids Research Database Issue

"The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema," has been published in the latest issue of Nucleic Acids Research.

The article describes the software architecture, database content and schema of the beta site. The query and analysis tools available are detailed.

The abstract and full text of the article are also available from the Nucleic Acids Research Web site.

Nita Deshpande, Kenneth J. Addess, Wolfgang F. Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John Westbrook, Helen M. Berman, and Philip E. Bourne The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema Nucl. Acids Res. 2005 33: D233-D237

21-December-2004

PDB Focus: Ligand Depot--a Small Molecule Information Resource

Ligand Depot (http://ligand-depot.rutgers.edu) is a data warehouse that integrates databases, services, tools, and methods related to small molecules bound to macromolecules.

An important tool to use when depositing PDB structures, this resource can be used to find codes for existing ligands, to link to other entries with a particular ligand, and to search for substructures.

If a ligand related to a deposition is not in Ligand Depot, please email the chemical diagram, name, and formula to deposit@rcsb.rutgers.edu.

Ligand Depot: a data warehouse for ligands bound to macromolecules

Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, and John Westbrook. (2004) Bioinformatics 20, pp. 2153-2155

http://bioinformatics.oupjournals.org/cgi/content/abstract/20/13/2153

14-December-2004

PDB Focus: Worldwide Data Annotation

PDB data are processed by an international effort involving members of the wwPDB -- RCSB, MSD-EBI, and PDBj.

Structures deposited using ADIT are annotated by staff from the RCSB (at Rutgers University in New Jersey and remotely at the Academy of Sciences of the Czech Republic) and PDBj in Osaka, Japan.

AutoDep depositions are processed by the MSD-EBI team in the United Kingdom.

Suzanne Richman on a visit to PDBj
RCSB annotator Suzanne Richman on a visit to PDBj, where she is currently processing data. From left to right: Shinobu Saeki, Yumiko Kengaku, Reiko Igarashi, Suzanne Richman, Yasuyo Morita, and Takashi Kosada.

07-December-2004

Open House at RCSB-Rutgers on Thursday, December 9, 2004

The RCSB-Rutgers site invites our local community to an open house on December 9 from 4:00 - 6:00 PM.

This event will celebrate the opening of the Molecular Wall Mural Exhibit by artist Jessica Milazzo and offer tours and demonstrations of the RCSB PDB.

The RCSB PDB is located in Doolittle Hall on the Busch Campus, behind the Department of Chemistry & Chemical Biology in Wright-Rieman Laboratories. Questions should be directed to info@rcsb.org or 732 445 0103 (phone).

07-December-2004

RCSB Beta Site Focus: Using PubMed Abstracts

Under an agreement with the National Library of Medicine, PubMed abstracts for the primary citation for structures in the RCSB PDB database are now available on this beta site. For any given structure, the PubMed abstract can be accessed from the Structure Explorer Summary Page by clicking on the PubMed link under the Primary Citation. A web page is returned with the article title, abstract, keywords, authors, organizational affiliation, journal, and PubMed identifier. The PubMed abstract at NCBI can be viewed by clicking on its icon.

The text box at the bottom of this page can be used to search for structures in the PDB using any word in the abstract or keyword fields. Terms can be entered into the text box either by typing the word manually or by clicking the mouse over any word in the abstract or the keyword fields. This provides an alternative means to finding structures of interest.

Any comments and suggestions about this or any other feature the beta site can be sent to betafeedback@rcsb.org.

Annual Report 2004

30-November-2004

RCSB PDB's 2004 Annual Report Now Available

We are pleased to announce that the RCSB Protein Data Bank's Annual Report, which covers the period of July 1, 2003 - June 30, 2004, is currently being distributed.

This annual snapshot of the RCSB PDB is intended to provide background information about the resource and describe recent progress and accomplishments. Available online as a PDF, this report is one of the many RCSB publications designed to keep our user community informed and involved. We hope that you will enjoy reading this report, and that you will send your correspondence or inquiries to info@rcsb.org.

23-November-2004

Publication of "PDBML: the representation of archival macromolecular structure data in XML"

A paper discussing the PDB exchange dictionary and the PDB archive files (collectively named "PDBML") has been published online.

PDBML files are available from ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML/.

John Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, and Helen M. Berman
PDBML: the representation of archival macromolecular structure data in XML Bioinformatics

23-November-2004

Oral History of PDB Archived with the Chemical Heritage Foundation

RCSB PDB Director Helen M. Berman was interviewed by David Berol (currently a writer for the Eastern Research Group) to discuss the rich history of the Protein Data Bank. Since her beginning days as a crystallographer, Berman believed that protein structure data should be available for archiving and sharing. In this interview, she discusses how the PDB was established at Brookhaven National Laboratory, the impact of community and technology on the archive, and the PDB's transition to the RCSB. Access to this oral history can be arranged through the Chemical Heritage Foundation

16-November-2004

RCSB PDB Exhibit at International Conference on Structural Genomics

The RCSB PDB will be exhibiting at the 2004 International Conference on Structural Genomics in Washington, DC (November 17-21). Please stop by booth 210 with any questions or comments, and to review the latest RCSB PDB materials.

16-November-2004

RCSB PDB's Art of Science Exhibit at Fairleigh Dickinson University

In celebration of National Chemistry Week, the RCSB PDB's Art of Science exhibit will be at Fairleigh Dickinson University in Teaneck, NJ.

Sponsored by the School of Natural Sciences and the Weiner Library of Fairleigh Dickinson University and the Hudson Bergen Chemical Society, the opening reception will be held November 19 at 5 p.m at the Weinder Library. The exhibit will run until December 19.

09-November-2004

New Data CD Release

The October 2004 release of PDB data on CD-ROM, Release #110, is shipping now. Two products make up the October 2004 release:
  • Release 110U contains the incremental set of experimentally determined structures (1,605) and models (30) deposited between July 1, 2004 and October 1, 2004, on a single disk.
  • Release 110U-EXP contains the experimental data, both x-ray structure factors (921) and NMR constraints (106), deposited between July 1, 2004 and October 1, 2004, on two disks.
Files for entries re-released for any reason between July 1, 2004 and October 1, 2004 are included in this release. A listing of files that have become obsolete since the last release is included so users can update their entire set of structures. Index files included in the pub/resource sub-directory contain all structures in the current PDB FTP site as of October 1, 2004.

NOTE: Demand has exceeded our supply of some January and April data CD releases. Releases 107F, 107F-EXP, 107U-EXP, 108U, and 108U-EXP are no longer available. New users may request remaining 2004 data CDs while supplies last. Don't forget to renew your PDB data CD subscription for 2005.

Further details and ordering information are available here. Questions should be directed to pdbcd@rcsb.org.

09-November-2004

Cryo-EM Workshop held at RCSB-Rutgers

A workshop was held to develop community consensus on the data items needed for deposition of 3D density maps and atomic models derived from cryo-electron microscopy studies. Organized by Helen M. Berman (Rutgers, The State University of New Jersey), Wah Chiu (Baylor College of Medicine), and Michael Rossmann (Purdue University), the Cryo-Microscopy Structure Deposition Workshop was held at RCSB-Rutgers in Piscataway, NJ (October 23-24, 2004). The workshop examined the data items currently collected by EMDep and ADIT for such depositions and discussed desirable additions in the near future. The presentations made are available from the meeting website at http://rcsb-dev.rutgers.edu:5015.

The workshop was sponsored by the RCSB PDB and the Computational Center for Biomolecular Complexes.

02-November-2004

RCSB Beta Site Focus: Searching the PDB based on NMR Experimental Details

In early July, the RCSB PDB released this newly reengineered beta site for public testing.

A new SearchFields feature available from this site is the ability to search for structures based upon specific NMR experimental parameters. These include NMR Experiment Type, Refinement Method, Selection Criteria, Spectrometer Manufacturer, Spectrometer Model, and Sample Conditions (for pH and Degrees Kelvin).

As with the current production site, searches may also be performed based upon experimental technique and the availability of constraint files.

Any comments and suggestions about the beta site may be sent to betafeedback@rcsb.org.

26-October-2004

Fall Newsletter Published

The Fall 2004 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. This issue describes RCSB workshop activities, including "A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools," which was aimed at depositors and "X-rays, Molecules, and You," which was intended for teachers and students.

Highlights also include a "Community Focus" article featuring PDBj Director Haruki Nakamura, and an look at the websites related to the "Database Challenges in Biology" symposium.

If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to info@rcsb.org. Email subscription information is available at http://www.rcsb.org/pdb/forum.html.

19-October-2004

Design and Content of RCSB PDB Data Deposition Services Enhanced

The RCSB PDB has further developed the web pages that describe data deposition. The main page at deposit.pdb.org links to the software and resources that can be used for preparing, checking, validating and depositing structural data to the PDB. It also provides individual guidelines for preparing structures determined by X-ray crystallography, NMR, or electron microscopy.

Tutorials are available for ADIT, PDB_EXTRACT, Validation, and Ligand Depot. A guide for converting a structure factor file into mmCIF format is also available.

A FAQ is provided to answer questions on a variety of subjects -- deposition, update, and release policies (such as "How do I replace coordinates?"), How do I ... ("How do I deposit a new chemical component/ligand?"), ADIT ("How can I base a new deposition on an older one?"), Validation ("I keep getting an error message -- what could be wrong?"), and PDB_EXTRACT ("What does PDB_EXTRACT do?").

It is recommended that all depositors review this page and its associated links in order to make their data deposition process quicker, easier, and more complete and accurate. We welcome your comments on these pages at deposit@rcsb.rutgers.edu.

12-October-2004

PDB_EXTRACT and data deposition tools described in Acta D paper

The options, procedures, and tools for accurate and automated PDB deposition are discussed in a recently published paper. PDB_EXTRACT, the PDB Validation Suite, and ADIT are highlighted.

Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
H. Yang, V. Guranovic, S. Dutta, Z. Feng, H. M. Berman and J. D. Westbrook
Acta Cryst. (2004). D60, 1833-1839
http://journals.iucr.org/d/issues/2004/10/00/be5021/index.html

05-October-2004

RCSB Beta Site Focus: Database Browsers

In early July, the RCSB PDB released this newly reengineered beta site for public testing. A major feature of the beta site is the ability to easily browse through database content based on the categories Biological Process, Cellular Component, Molecular Function, Enzyme Classification, Source Organism, Disease, Genome, SCOP Classification, CATH Classification, and Mutant Resource.

Each browser provides a hierarchical view of all the structures that are associated with the particular category or classification. Users can explore the category's hierarchy, view the number of associated PDB structures, and search for specific associated structures. The browsers are available from the left hand navigation bar and from the Search Fields menu items on the beta site. Detailed help and browsing examples are available via the integrated RoboHelp.

Any comments and suggestions about the browsers or any other beta site features may be sent to betafeedback@rcsb.org

28-September-2004

RCSB PDB Poster Prize awarded at AsCA meeting

Thanks to the students and judges who participated in the RCSB Poster Prize competition at ECM 22 (August 26-31 2004; Budapest, Hungary). The prize is designed to recognize student poster presentations involving macromolecular crystallography.

The prize was awarded to Jacques-Ph. Colletier for the poster "Kinetic crystallography on the cholinesterases" (J.P Colletier,a A. Royant,b A. Specht, c F. Nachon,d G. Zaccai,a M. Goeldner,c J.L Sussman,e I. Silman,f D. Bourgeois,b and M. Weik.a aLBM & bLCCP, IBS, Grenoble, France; cLCB, ULP, Strasbourg, France; dUE, CRSSA, La Tronche, France; e DSB & fDNB, WIS, Rehovot, Israel).

Special thanks to the judges of all of the student posters at ECM -- Matthias Bochtler, Zsolt Bocskei, Stefania Di Marco, Andrea Hadfield, and the Chair, Vilmos Fulop.

The RCSB PDB Poster Prize contest will resume in 2005 - further details will be announced in RCSB PDB web site news.  

Art of Science Exhibit

21-September-2004

RCSB PDB Art of Science Exhibit Part of EMBL-Hamburg's "Structural Biology at Crossroads: From Biological Molecules to Biological Systems"

EMBL-Hamburg hosted the conference "Structural Biology at Crossroads: From Biological Molecules to Biological Systems" on September 15-18. An exhibition of the RCSB PDB's Art of Science gallery show was opened during the second evening of the meeting with a presentation by RCSB PDB Director Helen M. Berman. Some of the best movies from the protein structure world were also shown.

The exhibit will be on display in the DESY Bistro (Notkestr. 85, Hamburg, Germany) until October 03, 2004.

14-September-2004

"The Impact of Structural Genomics on the Protein Data Bank" Published

A paper describing structural genomics' effects on the PDB's data pipeline, data capture, and target tracking has been published in American Journal of PharmacoGenomics:
The Impact of Structural Genomics on the Protein Data Bank
Helen M. Berman and John Westbrook
Am. J. Pharmacogenomics 2004; 4:247-252

07-September-2004

RCSB PDB Flyer: 5 Easy Steps for Crystal Structure Deposition

A PDF brochure describing the steps for crystal structure deposition is available for download.

The 5 steps for depositing crystal structures are:

 
  1. Use the PDB_EXTRACT Program Suite (available on the Web and as a software download)
  2. Check your structure with the PDB Validation Suite (available on the Web and as a software download)
  3. Run BLAST (at NCBI)
  4. Use Ligand Depot
  5. Deposit your structure using ADIT (available on the Web at RCSB-US, PDBj, and as a software download)

31-August-2004

Database Challenges in Biology

Symposium: Database Challenges in Biology

On September 10, 2004, "Databases Challenges in Biology" will bring together experts in biological data management to describe how data are organized in ways to enable scientists to derive new knowledge about structure and function.

This symposium, sponsored by the RCSB PDB, will be held at the Center for Advanced Research in Biotechnology (CARB) in Rockville, MD. Speakers and presentations will be:

  • Stephen Bryant, "Conserved Domain Database: A Protein Family Database"
  • Wah Chiu, "Database for Cryo-Electron Microscopy"
  • Mark Ellisman, "Multi-scale Imaging and Databasing of the Nervous System with Advanced Cyberinfrastructure"
  • John Johnson, "VIrus Particle ExploreR (VIPER): a Database of Standardized Atom Coordinates for Icosahedral Viruses and Dervied Descriptions of Subunit Interactions"
  • John Markley, "Data Management in the Laboratory: User Facilities and Research on Small and Large Scales"
  • Cathy Wu, "PIR Integrated Bioinformatics for Functional Genomics and Proteomics"
  • Helen Berman, "The RCSB Protein Data Bank: An Integrated Resource for Structural Biology"
The symposium is free, but seating is limited. Registration information is available at http://xpdb.nist.gov/challenges.

24-Aug-2004

New Data CD Release

The July 2004 release of PDB data on CD-ROM, Release #109, is shipping now. Two products make up the July 2004 release:

  • Release 109U contains the incremental set of experimentally determined structures (1,499) and models (40) deposited between April 1, 2004 and July 1, 2004, on a single CD-ROM disk.
  • Release 109U-EXP contains the experimental data, both x-ray structure factors (896) and NMR constraints (99), deposited between April 1, 2004 and July 1, 2004, on a single CD-ROM disk.

Files for entries re-released for any reason between April 1, 2004 and July 1, 2004 are included in this release. A listing of files that have become obsolete since the last release is included so users can update their entire set of structures. Index files included in the pub/resource sub-directory contain all structures in the current PDB FTP site as of July 1, 2004.

NOTE: Demand has exceeded our supply of some January and April data CD releases. Releases 107F, 107F-EXP, 108U, and 108U-EXP are no longer available. New users may request remaining 2004 data CDs while supplies last. Don't forget to renew your PDB data CD subscription for 2005.

Further details and ordering information are available here. Questions should be directed to pdbcd@rcsb.org.

17-Aug-2004

PDB Focus: How are HPUB structures released?

The release status of a structure is determined at the time of deposition by the author. The status HPUB is used to indicate that a structure will be released when the corresponding journal article is published. Publication is considered to be when the article is distributed by the publisher, either in print or electronically. The RCSB emails the depositor to either confirm that the publication corresponds to the structure, or to indicate that the structure will be released because the article includes the PDB ID.

The PDB receives publication dates and citation information from some journals. For other journals, the PDB scans the literature for publication information. We also greatly appreciate the citation information that is sent to us at deposit@rcsb.rutgers.edu from the community.

10-Aug-2004

RCSB PDB at Protein Society Meeting

The RCSB PDB will be presenting a poster "Protein Data Bank - Current State and Proposed Transition to a Re-engineered Query System" at the 18th Symposium of the Protein Society (August 14-18, 2004, San Diego Marriot Hotel) during the poster session on August 15th. Please stop by and say hello.

10-Aug-2004

Presentations from the ACA Workshop "A Protein Crystallographic Toolbox: CCP4 Software Suite and PDB Deposition Tools Available Online"

Together with CCP4, a session aimed at depositors entitled "A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools" was held during this year's ACA meeting. The presentations from this workshop have been made available at http://www.ccp4.ac.uk/courses/ACA2004/ACAworkshop04.html, including "An Introduction to the CCP4 Software Suite", "PDB_Extract and CCP4: Making Deposition Easier", and "Validation and Deposition at the RCSB Protein Data Bank".

03-Aug-2004

ACA Report: Poster Prize Awarded; Presentations, Demonstrations, and Workshops

The RCSB PDB would like to thank everyone who made this year's meeting of the American Crystallographic Association (ACA) such a success. Highlights included:

RCSB PDB Poster Prize: The RCSB PDB Poster Prize was awarded to Ty Adams for "The Crystal Structure of Factor Va: A New Mechanism for Membrane Binding and Function"

T.E. Adams1, M.F. Hockin2, K.G. Mann1, S.J. Everse1
1College of Medicine, University of Vermont, Burlington, VT 05401 2Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112.

The award will be Biochemistry - Vol. I by Donald and Judith G. Voet and a signed copy of Introduction to Macromolecular Crystallography by Alexander McPherson.

Special thanks to the students who participated, and to the judging committee as organized by Edward J. Collins - Jung-Ja Kim (Chair), Richard Brennan, Carolyn Brock, John Chrzas, and Nick Sauter.

The RCSB PDB Poster Prize will also be awarded to the best student poster presentation at this year's European Crystallographic Association (ECM) meeting.

RCSB Poster Prize winner from ACA Ty Adams
RCSB Poster Prize winner from ACA Ty Adams
 

Poster Presentation - 5 Steps for Crystal Structure Deposition. Annotator Kyle Burkhardt presented a poster entitled "Deposition and Annotation at the RCSB PDB". A brochure that summarizes this poster into "5 Steps" for crystal structure deposition is available for download (PDF)

Annotator Kyle Burkhardt at the ACA poster session
Annotator Kyle Burkhardt at the ACA poster session

Workshops. A report on the workshop for high school students and teacher "X-rays, Molecules, and You" will be available in the RCSB PDB's upcoming fall newsletter.

Together with CCP4, a session aimed at depositors entitled "A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools" was held.

Some members from RCSB and CCP4
Some members from RCSB and CCP4 at "A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools": back row: Roberto Steiner, Stuart McNicholas, Peter Briggs, Gywndaf Evans, Judith L. Flippen-Anderson. front row: Paul Emsley, Kyle Burkhardt, Shuchismita Dutta

Exhibit Booth and Demonstrations. The RCSB PDB was part of "Data Alley" in the exhibition hall, along with booths from CCP4 and CCDC. Demonstrations of the reengineered RCSB PDB beta site were given, along with demonstrations of data processing software. Thanks to everyone who stopped by!

RCSB member Huanwang Yang
RCSB member Huanwang Yang discusses PDB_EXTRACT with Wolfram Tempel at the exhibit booth. The PDB_EXTRACT Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

27-July-2004

Summer Newsletter Published

The Summer 2004 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. This issue introduces the RCSB PDB beta site and describes the activities in data deposition and processing; data query, reporting, and access; outreach and education. Highlights from this issue include a "Community Focus" article featuring E-MSD group leader Kim Henrick, and an "Education Corner" installment by J. Ricky Fox (Murray State University) that discusses using Visualization Tools the classroom.

If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to info@rcsb.org. Email subscription information is also available online.

20-July-2004

Reengineered RCSB PDB site
Wolfgang Bluhm demonstrates the reengineered RCSB PDB site

RCSB PDB Presentations and Demonstrations at 3D SIG and ISMB/ECCB, July 29 - August 4, 2004 in Glasgow, Scotland

The RCSB Protein Data Bank will be actively participating in the following two bioinformatics meetings to be held at the Scottish Exhibition and Conference Centre in Glasgow, Scotland:

  • 3D SIG, the first meeting of the Special Interest Group on Structural Bioinformatics, July 29-30, 2004.
  • The joint meeting of Intelligent Systems for Molecular Biology (ISMB) and the European Conference on Computational Biology (ECCB), July 31 - August 4, 2004.

In particular, RCSB PDB staff members will participate in the following presentations:

  • Software demo: "PDB-in-a-Box" (stand-alone laptop version of the reengineered RCSB PDB) by Wolfgang F. Bluhm on behalf of the RCSB PDB team (laptop session of 3D SIG, to be held following lunch on both July 29 and July 30, abstract number 8, full abstract.)
  • Oral presentation: "The Study of Evolution through Protein Domain Structure" by Song Yang, Russell Doolittle, Philip E. Bourne (July 30, 6pm, program schedule.)
  • Software demo: "MSD/RCSB PDB Access Tools and Databases" by the European Bioinformatics Institute and the Research Collaboratory for Structural Bioinformatics (August 1, 11:30am - 1:30pm, demo schedule.)
  • Oral presentation: "Program Chairs' Introduction: Databases" by Philip E. Bourne (August 4, 9:20am - 9:40am, program schedule.)
  • Poster: "The Reengineered RCSB Protein Data Bank: New means of data query and distribution" by Wolfgang F. Bluhm on behalf of the RCSB PDB team (poster number C-68, August 1-4, full abstract.)

13-July-2004

RCSB PDB Poster Prize awarded at AsCA meeting

Thanks to the students and judges who participated in the RCSB PDB Poster Prize competition at at this year's Conference of the Asian Crystallographic Association (AsCA; June 27-30, 2004, Hong Kong, China).

Chin-Yu Chen received the award for the poster entitled "Probing the DNA Kink Structure Induced by the Hyperthermophilic Chromosomal Protein SAC7D Using Site-Directed Mutagenesis and X-Ray Crystallography" (Chin-Yu Chen,a,c Ting-Wan Lina, Chia-Cheng Chou,a,b Tzu-Ping Koa, and Andrew H.-J. Wanga,d
aInstitute of Biological Chemistry and bCore Facility X-ray Crystallography, Academia Sinica, Taipei 115, Taiwan; cDepartment of Chemistry and dInstitute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.

The award will be Biochemistry - Vol. I by Donald and Judith G. Voet and Introduction to Macromolecular Crystallography by Alexander McPherson.

Special thanks to the AsCA RCSB PDB Poster Prize Committee as organized by Peter Colman.

The RCSB PDB Poster Prize will also be awarded to the best student poster presentation at this year's ACA and ECM meetings.  

06-July-2004

Come visit us in "Data Alley" -- RCSB PDB Demonstrations, Poster Prize, Workshops, and More at the ACA Annual Meeting July 17-22 in Chicago, IL

The RCSB PDB will be actively participating in the Annual National Meeting of the American Crystallographic Association (ACA) that will be held at the Hyatt Regency Hotel and Conference Center in downtown Chicago from Saturday, July 17 to Thursday, July 22, 2004. Highlights include:

Exhibit Booth and Demonstrations
. The RCSB PDB will be part of a "Data Alley" in the exhibition hall, along with CCP4 and CCDC. RCSB PDB members will be on hand to answer your questions and provide demonstrations of deposition software. Demonstrations of the reengineered RCSB PDB website and search engine will be featured during the morning and afternoon coffee breaks on Sunday, Monday, and Tuesday (July 18-20).

Workshops
. Two workshops will be held during the meeting. "A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools" will be held at the Hyatt Hotel on Saturday, July 17. "X-rays, Molecules, and You" (Sunday, July 18) is a workshop for high school teachers and students that include presentations on crystallography and examples of how you can use this information in your classroom. Participants are invited to attend the commercial exhibition and poster session.

RCSB PDB Poster Prize
: The RCSB PDB Poster Prize will be awarded to the best student poster presentation at this year's meeting. Students indicated their interest in participating as part of their abstract submission. The award will consist of two educational books that will be mailed to the winner after the meeting. An announcement will appear on the website and newsletter. The RCSB PDB Poster Prize will also be awarded at the European Crystallographic Association (ECM) meeting.

Poster Presentation
. On Tuesday (July 20), "Deposition and Annotation at the RCSB PDB" will be presented during the poster session (P147). We look forward to seeing the crystallographic community at this meeting.

29-June-2004

Links to the OCA Data Browser Available

OCA is a structure/function retriever and browser developed by Jaime Prilusky at the Weizmann Institute of Science. In addition to searching and browsing PDB data, OCA integrates data from other resources including GPCRDB, KEGG, OMIM, PDB select, Pfam, PubMed, SCOP, and Swiss-Prot. OCA mirror sites can accessed from http://www.rcsb.org/pdb/mirrors.html#OCA_PDBLite.

22-June-2004

Batch File Download Script Now Available

A script to download large numbers of files from the PDB FTP site is now available at ftp://ftp.rcsb.org/pub/pdb/software/getPdbStructures.pl

This simple Perl script can be run locally to download files from the user's list of PDB IDs. Options are available to download coordinate files in either PDB or mmCIF format, as well as experimental data files. The script creates a divided directory structure for the downloaded files. Further details regarding usage of this script can be found at ftp://ftp.rcsb.org/pub/pdb/software/getPdbStructures.html.

15-June-2004

PDB extract logo

RCSB PDB Poster Prize to be Awarded at AsCA -- Instructions for Entering

The RCSB PDB Poster Prize will be awarded to the best student poster presentation at this year's Conference of the Asian Crystallographic Association (AsCA; June 27-30, 2004, Hong Kong, China).

Presenters wishing to enter should collect the "PDB" sticker from the AsCA registration desk or the IUCr exhibit stand and affix it to their poster. At a suitable time during the session the RCSB PDB Poster Prize Committee will judge the 'best' poster from among those with stickers.

The award will consist of two educational books that will be mailed to the winner after the meeting. An announcement will appear on the PDB web site and in the PDB Newsletter, and in the ACA and IUCr Newsletters.

The RCSB PDB Poster Prize will also be awarded at the the American Crystallographic Association (ACA) and the European Crystallographic Association (ECM) meetings.  

15-June-2004

Legacy AutoDep Deposition System Closing at RCSB

RCSB support for the legacy BNL AUTODEP deposition system will cease on August 15, 2004. After this point this deposition system and all stored session files will be unavailable. Depositions to the RCSB PDB can be made using the ADIT system at http://deposit.pdb.org/adit. A version of AUTODEP will continue to be maintained by the MSD EBI group at http://www.ebi.ac.uk/msd/Deposition/Autodep.html.

08-June-2004

PDB extract logo

PDB_EXTRACT integrated into CCP4 Program Suite

PDB_EXTRACT, a program suite that contains tools and examples for extracting mmCIF data from structure determination applications, has been integrated with the CCP4i interface of the CCP4 program suite for protein crystallography (version 5.0).

PDB_EXTRACT is also available in binary and source distributions from http://pdb.rutgers.edu/mmcif/PDB_EXTRACT/index.html.

PDB_EXTRACT extracts information about data processing, heavy atom phasing, molecular replacement, density modification, and final structure refinement from the output files produced by many X-ray crystallographic applications. The program merges these data into macromolecular Crystallographic Information File (mmCIF) data files that can be used with ADIT to perform validation and to add any additional information for PDB deposition. An online version of pdb_extract is available at http://pdb-extract.rutgers.edu/ .

1-June-2004

TargetDB and Ligand Depot papers published in Bioinformatics

Two papers have been published online that describe the TargetDB and Ligand Depot resources. TargetDB is a centralized target registration database that includes protein target data from the NIH structural genomics centers and a number of international sites. Ligand Depot is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids.

Li Chen, Rose Oughtred, Helen M. Berman, and John Westbrook
TargetDB: a target registration database for structural genomics projects Bioinformatics

Zukang Feng, Li Chen, Himabindu Maddula, Ozgur Akcan, Rose Oughtred, Helen M. Berman, and John Westbrook
Ligand Depot: a data warehouse for ligands bound to macromolecules Bioinformatics

25-May-2004

"The Protein Data Bank and lessons in data management" published in Briefings in Bioinformatics

The history of the PDB is used to highlight practices important to developers of biological databases today in this article. The role of the "human factor" in the form of users, collaborators, scientific society, and ad hoc committees is also included.

Philip E. Bourne, John Westbrook, Helen M. Berman
The Protein Data Bank and lessons in data management
(2004) Briefings in Bioinformatics 5, pp 23-30.

Link to Briefings in Bioinformatics: http://www.henrystewart.com/journals/bib/

25-May-2004

STRUCTURAL BIOINFORMATICS (3D SIG)

A two day Structural Bioinformatics (3D SIG) Meeting will be held Thursday, July 29 through Friday, July 30 in
Glasgow, Scotland, immediately preceding ISMB/ECCB 2004.
3D SIG will include a mix of invited talks, short presentations (selected from the Laptop-session submission) and panel discussions.
Topics will include 3D data-mining, 3D programming modules, docking & protein-protein/ligand interaction prediction, membrane protein assembly prediction, secondary structure & domain assignment, structure-based function prediction, structural databases, structural genomics, structure prediction, structure representation, geometry & energetics in protein structure & function. Posters not competing for oral presentation will be accepted until June 30.

The RCSB PDB will demonstrate the reengineered RCSB PDB site as part of the laptop session.

More information is available at http://3dsig.weizmann.ac.il/

18-May-2004

Workshops at ACA Chicago Meeting

The RCSB PDB is involved with two workshops that will be part of the ACA's Annual Meeting in Chicago, IL (July 17-22, 2004).

* A Protein Crystallographic Toolbox: CCP4 Software Suite and RCSB PDB Deposition Tools

The RCSB PDB is co-sponsoring this workshop with CCP4. This all-day workshop will be held at the Hyatt Hotel on Saturday, July 17. The format of the workshop will be based around presentations on the CCP4 suite and its key programs (including Mosflm and Refmac), and on RCSB PDB Deposition Tools (including ADIT and PDB_EXTRACT). The workshop will focus on how PDB_EXTRACT works with the various programs in CCP4 to extract information needed for depositors. Opportunities for informal group discussions will be provided. Participants are encouraged to bring their own problem cases in the form of data, to be discussed either during or after the workshop.

The workshop is aimed primarily at less experienced users who are familiar with protein crystallography but less familiar with the CCP4 and RCSB PDB packages. More experienced users may also benefit from the sessions on individuatl programs, and the opportunity to interrogate the individual program developers.

The cost for students is $80, and $100 for all others. Please register by selecting the workshop box on the ACA registration form.
Questions may be sent to info@rcsb.org or ccp4@ccp4.ac.uk.

The RCSB PDB is sponsoring a workshop for students and teachers in the Chicago area as part of the annual ACA Meeting. The workshop, including lunch, will be free but attendance is limited and pre-registration is required.

* X-rays, Molecules, and You

Single molecules are the building blocks of life. Crystallography, the science that studies the structures of these molecules, is both fascinating and provocative, because it allows us to "see" these molecules and understand how they work. Once we know how molecules function, we can modify them to make them work better or we can try to fix them when they break. Crystallography has shown us that molecules are shaped in very special ways to get the job done. Understanding the shape of these molecules and how they interact with one another may hold the key to developing new medicines and materials.

The day will include presentations on the general basics of crystallography, on the wealth of information derived from crystallography contained in the databases that store 3-dimensional structural results and examples of how you can use this information in your classroom. Existing programs involving high school teachers and students for the rapid prototyping of molecular models will be described, along with mini-workshops on growing protein crystals, building molecular models, and hands-on interaction with the databases. There will also be an opportunity to visit commercial exhibits at the national meeting and a scientific poster session including posters prepared by high school students in the Chicago area.

For more information or questions send email to info@rcsb.org.

Links: CCP4 to http://www.ccp4.ac.uk/index.php
ACA Meeting to http://www.uic.edu/orgs/aca2004/
teacher workshop preregistration: http://www.rcsb.org/pdb/workshop.pdf

11-May-2004

FASTA Sequence Files on RCSB PDB FTP Archives

The RCSB PDB maintains several FASTA formatted sequence files on the FTP archives. The sequences for all currently released experimental structures are contained in pdb_seqres.txt, available in uncompressed form at ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt and in Unix compressed (".Z") format at ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt.Z. These two files contain all sequences for structures queried on the Home Page, QuickSearch, SearchLite, and SearchFields.

PDB depositors are given the opportunity to prerelease the sequences of their structures in advance of the release of the coordinates (see this previous news item). These prereleased sequencs for unreleased structures are contained in the separate file pre-released.seq, available in uncompressed form at ftp://ftp.rcsb.org/pub/pdb/derived_data/index/pre-released.seq. Unreleased structures can be queried on the Status Query page.

27-Apr-2004

RCSB PDB High School Workshop on Molecules in Chicago - July 18, 2004

The RCSB PDB is sponsoring a workshop for students and teachers in the Chicago area as part of the annual ACA Meeting. The workshop, including lunch, will be free but attendance is limited and pre-registration is required.

Single molecules are the building blocks of life. Crystallography, the science that studies the structures of these molecules, is both fascinating and provocative, because it allows us to "see" these molecules and understand how they work. Once we know how molecules function, we can modify them to make them work better or we can try to fix them when they break. Crystallography has shown us that molecules are shaped in very special ways to get the job done. Understanding the shape of these molecules and how they interact with one another may hold the key to developing new medicines and materials.

The day will include presentations on the general basics of crystallography, on the wealth of information derived from crystallography contained in the databases that store 3-dimensional structural results and examples of how you can use this information in your classroom. Existing programs involving high school teachers and students for the rapid prototyping of molecular models will be described, along with mini-workshops on growing protein crystals, building molecular models, and hands-on interaction with the databases. There will also be an opportunity to visit commercial exhibits at the national meeting and a scientific poster session including posters prepared by high school students in the Chicago area.

For more information or questions send email to info@rcsb.org.

27-Apr-2004

CD-ROM Subscriber Questionnaire Results Released

A short online questionnaire was emailed to 1450 RCSB PDB CD-ROM subscribers in February 2004. The purpose of this instrument was to get to know subscribers, ask their opinion on how well we are doing and gauge interest in a DVD data product.

The questionnaire had a 23% response rate. While the overall 84.5% approval rating from our subscribers is very good, there is room for improvement. Many respondents provided additional information in the comments section and took additional time to write us separately.

Problems are being addressed immediately. Suggestions for improvements are being reviewed and considered by RSCB PDB staff. Suggested improvements already in development include a top level index and a DVD data product. The results of the questionnaire have been compiled and are detailed in the CD-ROM Subscriber Questionnaire Results report.

20-Apr-2004

RCSB PDB Newsletter 21 Released

The Spring 2004 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. This issue describes the activities of the RCSB PDB during the past quarter in the areas of data deposition and processing; data query, reporting, and access; outreach and education. Highlights from this issue include a "Community Focus" article featuring RCSB PDB Director Helen M. Berman, and an "Education Corner" installment by Tommie S. Hata, a high school biology teacher, that describes how he has used the PDB in his classroom.

If you'd like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to info@rcsb.org. Email subscription information information is available here.

13-Apr-2004

RCSB Poster Prize awarded at RECOMB

Thanks to the students and judges who participated in the competition for the best student poster presentation in the category of "Protein Structure" at the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004; March 27-31, San Diego, CA).

The RCSB PDB Poster Prize was awarded to Boris E. Shakhnovich for the poster "Protein Structure and Evolutionary History Determine Sequence Space Topology"

Boris E. Shakhnovich1, Eric Deeds2, Charles Delisi1, and Eugene I. Shakhnovich3

1 Bioinformatics Program, Boston University
2 Department of Molecular and Cellular Biology, Harvard University
3 Department of Chemistry and Chemical Biology, Harvard University

13-Apr-2004

RCSB PDB at the Experimental Nuclear Magnetic Resonance Conference (ENC)

The RCSB PDB will have a tabletop display at the 45th Experimental Nuclear Magnetic Resonance Conference (ENC) to be held April 18 - 23 at the Asilomar Conference Center (Pacific Grove, CA). We will be in the Surf and Sand Living Room of the conference center -- please stop by and say hello.

06-Apr-2004

A new 'QuickSearch' feature is available

After a period of beta testing, a new "QuickSearch" feature is now available on all production sites. This is a new keyword search feature which searches across the PDB archive and/or the RCSB PDB website static pages. It supports the search syntax of the Lucene-based keyword search currently in production. An 'Exact Word Match' and 'Full Text' search is performed on an index of the mmCIF files and an index of the static RCSB PDB Web pages. The structures returned by the search can be browsed, refined and explored using the Query Result Browser and Structure Explorer. The static page results are listed as links and displayed with the keyword highlighted in the context in which it appears. Please write to info@rcsb.org with comments or suggestions.

30-Mar-2004

RCSB PDB at RECOMB and National Science Teachers Association's National Convention

RECOMB

A demonstration on using the re-engineered RCSB PDB web site will be given and an RCSB PDB Poster Prize will be awarded at the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004; March 27-31, San Diego, CA).

"Effective Use of the RCSB Protein Data Bank" will be demonstrated on Tuesday, March 30 by RCSB PDB Co-director Philip E. Bourne at 5:00 PM in the California Ballroom. Additionally, an RCSB PDB Poster Prize will be awarded to the best student poster in the category of "Protein Structure".

NSTA

The RCSB PDB will be participating at the National Science Teachers Association (NSTA) National Convention April 1-4, 2004 in Atlanta, GA. The RCSB PDB will be at the MSOE Center for BioMolecular Modeling's Exhibit Booth (633) to meet with science educators.

23-Mar-2004

PDB Focus: XML Data Files

All released PDB entries are available in XML format from the PDB beta FTP site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML/.

The XML data files have been created by software translation of the mmCIF data files (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/), as part of the PDB Data Uniformity Project. The mmCIF data files use the data items that are defined in the PDB Exchange Dictionary (http://deposit.pdb.org/mmcif/). The XML data files conform to an XSD-style XML Schema (http://mmcif.rcsb.org/dictionaries/ascii/pdbx.xsd) that is derived from the PDB Exchange Dictionary. As a result, the element and attribute names in the XML data files directly correspond to the item names defined the PDB Exchange Dictionary.

The delivery of PDB data in XML format is the product of the collaboration between the Protein Data Bank Japan (PDBj), the Macromolecular Structure Database (MSD) group at European Bioinformatics Institute (EBI), and the Research Collaboratory for Structural Bioinformatics (RCSB)--the three members of the Worldwide PDB (wwPDB; http://www.wwpdb.org).

Feedback on the XML data files is highly appreciated, and may be sent to info@rcsb.org.

16-Mar-2004

PDB Poster Prize, Demonstration at RECOMB 2004

A PDB Poster Prize will be awarded to the best student poster in the category of "Protein Structure" at the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004; March 27-31, San Diego, CA). The winner will receive a copy of Bioinformatics: The Machine Learning Approach (2nd edition), by Pierre Baldi and Soren Brunak.

A demonstration on "Effective Use of the RCSB Protein Data Bank" will be given on Tuesday, March 30 by PDB CoDirector Philip E. Bourne at 5:00 PM in the California Ballroom.

09-Mar-2004

A new 'QuickSearch' feature is available on the Beta site

This is a new keyword search feature which searches across the PDB archive and/or the PDB website static pages. It supports the search syntax of the Lucene-based keyword search currently in production. An 'Exact Word Match' and 'Full Text' search is performed on an index of the mmCIF files and an index of the static PDB Web pages. The structures returned by the search can be browsed, refined and explored using the Query Result Browser and Structure Explorer. The static page results are listed as links and displayed with the keyword highlighted in the context in which it appears. Please write to info@rcsb.org with comments or suggestions.

02-Mar-2004

Molecular Machinery Poster Available as PDF

The poster, "Molecular Machinery: A Tour of the Protein Data Bank" by David S. Goodsell is now out of print, so we are making the original PDF file available for download. You can download a 2-sided, 8 1/2" x 11" quick reference guide (5MB) or a 24" x 36" poster (31MB).

24-Feb-2004

New CD-ROM Release

The January 2004 release of PDB data on CD-ROM, Release #107, is shipping now.

Four separate products make up the January 2004 release:

  • Release 107F includes the full set of experimentally determined structures (23,792) and models (709) deposited in the PDB by January 1, 2004, on a six (6) disk set.
  • Release 107F-EXP contains the full set of experimental data deposited by January 1, 2004, both x-ray structure factors (11,469) and NMR constraints (1,790), on a nine (9) disk set.
  • Release 107U contains the incremental set of experimentally determined structures (1,357) and models (67) deposited between October 1, 2003 and January 1, 2004, on a single CD_ROM disk.
  • Release 107U-EXP contains the experimental data, both x-ray structure factors (886) and NMR constraints (93), deposited between October 1, 2003 and January 1, 2004, on two CD_ROM disks.

Files for entries re-released for any reason between October 1, 2003 and January 1, 2004 are included in this release. A listing of files that have become obsolete since the last release is included so users can update their entire set of structures. Index files included in the pub/resource sub-directory contain all structures in the current PDB FTP site as of January 1, 2004. NOTE: New subscribers will receive the January release of the current year and all subsequent updates while supplies last. Continuing subscribers will receive the quarterly update. Continuing subscribers will be sent full data sets upon request while supplies last. Questions should be directed to pdbcd@rcsb.org. Ordering information is available here.

17-Feb-2004

Release of ADIT-NMR Deposition Tool at BMRB

BMRB and PDB today announce the release of the new ADIT-NMR deposition tool available from the BMRB website (http://www.bmrb.wisc.edu). The current ADIT-NMR release provides the biological NMR community with a deposition interface for submitting a wide variety of quantitative experimental results from NMR spectroscopic studies of biological macromolecules to BMRB. The interface will be familiar to those who have submitted atomic coordinates and NMR constraints to the PDB. ADIT-NMR has been developed as a collaborative project between the RCSB members PDB and BMRB. Through the PDB/BMRB collaboration, the ADIT-NMR tool will soon become a one-stop site for the deposition of all NMR derived data including atomic coordinates and constraints. The tool combines the BMRB dictionary for NMR experimental results with the software platform created by the PDB for the ADIT deposition system to create an easy to use interface for submitting NMR spectral parameters (chemical shifts, J-coupling constants, residual dipolar couplings, etc.), relaxation parameters, hydrogen exchange and pKa data to the BMRB. All members of the biological NMR community are encouraged to make use of ADIT-NMR in depositing their data at BMRB and PDB.

10-Feb-2004

"The PDB: A case study in management of community data" published in Current Proteomics

A paper describing the development of the PDB and the systems in place for deposition and distribution, has been published in the inaugural issue of Current Proteomics (http://www.bentham.org/cp).

H.M. Berman, P.E. Bourne, J. Westbrook (2004): The Protein Data Bank: A case study in management of community data. Current Proteomics 1, pp. 49-57.

03-Feb-2004

"Validation of protein structures for the PDB" paper published in Methods in Enzymology

A paper describing the procedures used for structure validation and processing has been published in the Macromolecular Crystallography volume of Methods in Enzymology. An overview of the deposition process, including descriptions of the checks and reports generated by ADIT are provided. The validation and standardization of all the data in the PDB is also outlined.

J. Westbrook, Z. Feng, K. Burkhardt, H.M. Berman (2003): Validation of protein structures for protein data bank. Methods Enzymol. 374, pp. 370-85.

PDB Art of Science Exhibit Visits the University of Wisconsin-Madison

The PDB's Art of Science will be on display in the Biochemistry Atrium at the University of Wisconsin-Madison from February 5 - March 12. The exhibit is being sponsored by the Center for Eukaryotic Structural Genomics (CESG) and the BioMagResBank (BMRB). Contact Jurgen F. Doreleijers at jurgen@bmrb.wisc.edu for more information.

The PDB's Art of Science exhibit includes large-scale depictions of proteins and images and text from the Molecule of the Month series.

The exhibit was recently part of a Molecular Gallery Show at California State University Fullerton campus. In addition to PDB images, the show featured images from the PDB and 3-D models by David Goodsell and Arthur Olson (The Scripps Research Institute). Also included were objects from the Cal State Fullerton Keck Center for Molecular Structure, such as an older generation X-ray camera, a video station, X-ray camera and cases containing PDB's literatures and many teaching tools (mini 3-D models, tubers, water kit) purchased for the exhibits.

Art of Science exhibit Art of Science exhibit
The Art of Science at California State University Fullerton

27-Jan-2004

Protein Data Bank Opens New Era With Broader Support

The National Science Foundation has just announced a five-year renewal of funding for the PDB under the management of the RCSB. NSF has supported the PDB continuously since 1975, and a multi-agency support partnership first formed in 1989. For the past five years, that partnership has included NSF, the National Institute of General Medical Sciences (NIGMS), the Department of Energy (DOE) and the National Library of Medicine (NLM). The partnership has been expanded now to include the National Cancer Institute (NCI), the National Center for Research Resources (NCRR), the National Institute of Biomedical Imaging and Bioengineering (NIBIB), and the National Institute of Neurological Disorders and Stroke (NINDS).

The new support agreement, which began Jan. 1, calls for the PDB to continue to be managed by three members of the Research Collaboratory for Structural Bioinformatics (RCSB): Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the University of Maryland/National Institute of Standards and Technology's Center for Advanced Research in Biotechnology. This new era for PDB opens following the recent announcement of the wwPDB (http://www.wwpdb.org), an international agreement to coordinate the deposition and distribution of molecular structure data.

The PDB has continued to grow and to evolve since its inception in 1971: last year, more than 4,600 new molecular structures were added, and, on an average day, visitors downloaded various structural files more than 120,000 times. Over the next five years, the PDB will meet challenges that include the expanded integration of its information with other biological resources, keeping up with the increasing complexity and volume of deposited structures, meeting the demands for more complex queries, and providing more detailed annotation of the experiments and the structures. PDB also will also continue to serve an ever-expanding, diverse and global user community.

The NSF announcement is available at http://www.nsf.gov/od/lpa/news/04/pr0408.htm, along with these related materials:

A chronology of PDB and Structural Biology milestones - http://www.nsf.gov/od/lpa/news/04/fstimeline_pdb_04.htm
Examples and impacts of PDB structures - http://www.nsf.gov/od/lpa/news/04/fspdb_examples.htm
Images of PDB structures - http://www.nsf.gov/od/lpa/news/04/pr0408_images.htm
RCSB PDB, wwPDB and U.S. federal agency contacts - http://www.nsf.gov/od/lpa/news/04/fscontacts_pdb_04.htm

20-Jan-2004

RCSB PDB Newsletter 20 Released

The Winter 2004 issue of the RCSB PDB Newsletter is now available in HTML format at http://www.rcsb.org/pdb/newsletter/2003q4/. This issue describes the activities of the RCSB PDB during the past quarter in the areas of data deposition and processing; data query, reporting, and access; outreach and education. Highlights from this issue include a "Community Focus" article featuring Edward N. Baker, and an "Education Corner" installment by Katherine Kantardjieff.

If you'd like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to info@rcsb.org.

Molecule of the Month Highlighted in BAMBED

The PDB's Molecule of the Month feature was highlighted as "Website of Note" in Biochemistry and Molecular Biology Education (BAMBED; 2003: 31(5), p. 366). As stated in the article, "It is a great place for visitors to start their exploration of the fascinating world of structural biology." The Molecule of the Month installments can be found at http://www.rcsb.org/pdb/molecules/molecule_list.html.

13-Jan-2004

PDB Chemical Component Dictionary Format Description Available

The PDB is constantly improving its descriptions of small molecules.

The PDB Chemical Component Dictionary (formerly called the HET Group Dictionary) is available in PDB and mmCIF formats, and is updated weekly. This resource, created by the curation efforts of the PDB teams at Rutgers University and CARB/NIST, is under active development.

A guide to the formats used in the PDB Chemical Component Dictionary is available at http://deposit.pdb.org/cc_dict_tut.html. This guide provides descriptions and examples of the contents of the PDB and mmCIF format Chemical Component Dictionaries, as well as a description of the contents of entries in the Ligand Depot.

Ligand Depot (http://ligand-depot.rutgers.edu/) has been created as a data warehouse that integrates databases, services, tools and methods related to small molecules that are bound to macromolecules. It was created to help users explore the PDB Chemical Component Dictionary and the small molecule contents of the PDB.

Comments and suggestions on the PDB Chemical Component Dictionary, the format description guide, and Ligand Depot are greatly appreciated, and may be sent to info@rcsb.org.

06-Jan-2004

PDB entry 2hhb
In PDB entry 2hhb, the biological unit is 1 asymmetric unit.

PDB Focus: Accessing and Understanding Biological Units

When crystallographic structures are deposited in the PDB, the primary coordinate file generally contains one asymmetric unit - a concept that has applicability only to crystallography, but is important to understanding the process in obtaining the functional biological molecule. An introduction to biological units in the PDB archive is now accessible at http://www.rcsb.org/pdb/biounit_tutorial.html. This useful guide offers definitions of the terms 'asymmetric unit' and 'biological molecule', indicates where information about the biological unit can be found in PDB and mmCIF coordinate files, and describes how the biological unit files in the PDB have been derived.

Coordinate files for the biological units for applicable structures are accessible from the View Structure and Download/Display File sections of the Structure Explorer pages on the primary PDB web site and its mirrors. The biological unit coordinate files can also be downloaded from the PDB FTP site at ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/.

Images for the asymmetric and biological units are available from each entry's View Structure section of the Structure Explorer page.

Last Updated: August 06, 2004