RCSB PDB Newsletter Archive
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Editions for 2018
Issue 76 - January 2018
This issue reviews 2017 milestones and publications, improved text searching, and implementation of versioning for PDB data files. In the Education Corner, RCSB PDB summer interns describe their journey to ABRCMS.
Issue 77 - April 2018
Impact of the PDB archive, new and updated Validation Reports, new RCSB.org features, and more. The Education Corner looks at Creating sculptural models of proteins in a high-school engineering class.
Editions for 2017
Issue 72 - January 2017
Read about 2016 milestones and a review of recently-added website tools and features. The Education Corner describes a cyber-linked summer program training the next generation of computational structural biologists by Rebecca F. Alford & Jeffrey J. Gray (Johns Hopkins University).
Issue 73 - April 2017
NSF and Popular Science announcing Zika Virus painting as 'Vizzies' Winner, data management, and more. In the Education Corner, Merry Wang (Autodesk Research) presents 'Learning in Virtual Reality: Revolutionizing education with Autodesk's Molecule Viewer'
Issue 74 - July 2017
This issue celebrates Helen Berman's ACA award, describes upcoming changes to the FTP archive, and shows how to access structural variations using PDBFlex data. In the Education Corner, Molecule of the Month creator David Goodsell asks readers to Get Excited, Be Critical.
Issue 75 - October 2017
This issue introduces the 2017 User Survey; PDB-Dev, the prototype system for Integrative/Hybrid structural models, and improved text searching. The Education Corner reports on an educational symposium focused on Structural Databases as Teaching Tools.
Editions for 2016
2015 statistics and highlights, the new wwPDB Deposition Tool, RCSB PDB's 2016 protein-drug calendar, and more. The Education Corner describes Using 815,527 Crystal Structures to Teach Chemistry: The Cambridge Structural Database.
Wellcome Trust Image Awards, visualization of electron density maps for ligands, 2016 high school video challenge, and more. In the Education Corner, Jed Dannenbaum, a USC Professor of the Practice of Cinematic Arts gives advice on telling scientific stories with videos.
Meet our summer interns, watch the Video Challenge award winners, explore protein modifications in the PDB, and more. In the Education Corner, Krystle J. McLaughlin describes Lysozyme, Models and the PDB: Helping Undergraduates Explore Structure.
Learn about new website resources and access the new wwPDB Validation Server. In the Education Corner, Todd P. Silverstein (Willamette University) describes Myoglobin Structure and Function: A multi-week biochemistry laboratory project for undergraduates.
Editions for 2015
Read about 2014 statistics and highlights, large structures in the PDB, 15 years of the Molecule of the Month, and more. The Education Corner describes how teachers have Mentored High School Students for the RCSB PDB HIV Video Challenge.
Read about the new Molecular Machinery viewer, released just as the PDB reached 100,000 protein entries, large structures in the PDB, a paper describing the Chemical Component Dictionary, BioJava, and more. The Education Corner highlights an online resource about HIV biology.
Articles describe the RCSB PDB's leadership transition anniversary, new website features for query and visualization, and the protein modeling results at the National Science Olympiad. RCSB PDB remembers Edgar Meyer and John Wooley. The Education Corner highlights the results of our High School Video Challenge.
Articles describe new website features for visualization and analysis, an important Hybrid/Integrative Methods publication, 2015 Poster Prize roundup, and more. The Education Corner explores Learning the ABCs of Proteins.
Editions for 2014
Editions for 2013
Issue 59 - October 2013 (HTML)
This newsletter describes the recent wwPDB Symposium: A Celebration of Open Access in Structural Biology, recent deposition and website statistics, ligand report options, new features added to the RCSB PDB and PDB-101 websites, and an update on the new wwPDB Deposition & Annotation System.
Issue 58 - July 2013 (HTML |
Highlights wwPDB News, upcoming meetings, and more. The Education Corner highlights the RCSB PDB's visit to the National Science Teachers Association meeting.
Issue 57 - April 2013 (HTML |
Describes new website features, the Biologically Interesting molecule Reference Dictionary, and more. The Education Corner highlights the RCSB PDB help desk.
Issue 56 - January 2013 (HTML |
Explores the 2012 Annual Report, 2012 deposition and access statistics, how to visually map PDB structures to sequences, and more. The Education Corner describes molecular visualization tools developed for browers and mobile devices by Takanori Nakane (Kyoto University). Nakane's program NDKmol is part of theRCSB PDB Mobile app.
Editions for 2012
Issue 55 - Fall 2012 (HTML |
heads back to school with PDB-101, looks at deposition tools pdb_extract and SF-Tool, and describes the RCSB PDB Mobile app. The Education Corner details the University of Georgia's Biotech Boot Camp for high school teachers.
Issue 54 - Summer 2012 (HTML |
explores new website features, RCSB PDB Mobile, and 150 Molecule of the Month columns. The Education Corner looks at how students are Learning Science by Doing Science at the Waksman Student Scholars Program.
Issue 53 - Spring 2012 (HTML |
includes a look at a special molecular animation, depositing structures for Foldit, browsing the PDB archive, and more. The Education Corner discusses Project CRYSTAL: Crystallographers Researching with Young Scientists, Teaching and Learning.
Issue 52 - Winter 2012 (HTML |
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.
Editions for 2011
Issue 51 - Fall 2011 (HTML |
Explores the new pdb_extract and SF-Tool updates, the latest website release, new additions to PDB-101, and the latest on the PDB40 symposium. In the issue's Education Corner, Christopher Smith (Center for Theoretical Biological Physics at UCSD) gives his Insights into Molecular Modeling for the Middle Schooler. The newsletter also describes the many ways users can explore new entires, recent RCSB PDB poster prize awardees, new website and deposition statistics, and more.
Issue 50 - Summer 2011 (HTML |
This issue highlights PDB 40's program, poster session, and travel awards along with the latest developments in data deposition, data query, and outreach and education. The Education Corner focuses on the American Association for the Advancement of Science's report Vision and Change in Undergraduate Biology Education: A Call to Action. The newsletter also describes new options for generating Validation Reports, and highlights the Browse Database option of exploring the PDB archive using hierarchal trees organized by GO terms, EC number, source organism, and more.
Issue 49 - Spring 2011 (HTML |
This issue highlights the upcoming PDB 40 symposium, synchrotron news, options available for exploring PDB entries, and more. In the Education Corner, New Jersey high school teacher Richard Tempsick describes how he builds proteins structures and uses the Molecule of the Month in the classroom.
Issue 48 - Winter 2011 (HTML |
The year 2010 through data deposition, website traffic, and Molecules of the Month. This issue also highlights the latest website release, recent meeting activities, the 2010 Annual Report PDF, and more.
Editions for 2010
Issue 47 - Fall 2010 (HTML |
This issue highlights the Molecule of the Month and the topic categories. In the Education Corner, Joan Kiely (Stony Brook University ) describes the Stony Brook University Protein Challenge, a competition for high school students that helps them understand the structure and function of proteins.
Issue 46 - Summer 2010 (HTML |
This issue highlights new website advanced search and reporting options. In the Education Corner, Phil McFadden (Oregon State University) describes Protein Portraits, a nontraditional college course developed around the question of what it might be like to shrink to the nanometer realm for a direct encounter with a protein molecule.
Issue 45 - Spring 2010 (HTML |
This issue highlights new website features and the comprehensive suite of RCSB PDB training materials. In the Education Corner, A Proficiency Rubric for Biomacromolecular 3D Literacy is presented.
Issue 44 - Winter 2010 (HTML |
This issue highlights 2009 deposition, release, and access statistics, describes new website features for searching and reporting, and reviews recent outreach activities. In the Education Corner, IJsbrand M. Kramer discusses the benefits of using more "realistic" molecular images in university cell biology courses.
Editions for 2009
Issue 43 - Fall 2009 (HTML |
In the Education Corner, Gary Battle reports on a recent symposium that demonstrated the different ways the Cambridge Structural Database is used to teach chemistry. In the Community Focus, Roland Dunbrack, Jr. (Fox Chase Cancer Center) discusses his research in computational structural biology and the software his laboratory makes available for download.
Issue 42 - Summer 2009 (HTML |
The new features and functionality that have been added to www.pdb.org are highlighted. In the Community Focus, Gregory Warren discusses the worlds of modeling and crystallography. Recent outreach activities, along with data deposition and data query news, are also available.
Issue 41 - Spring 2009 (HTML |
In this issue, David Goodsell interviews molecular animators Gaël McGill and Graham Johnson to find out how PDB data gets translated into their detailed movies and images. In the Education Corner, Gavin Whittaker describes how physical models can be created and used to provide a unique view of molecular structure. New RCSB PDB features and developments, including the recent release of MyPDB email alerts, are highlighted.
Issue 40 - Winter 2009 (HTML |
This edition offers tips for depositing multiple related structures and describes the release of PDB Archive Version 3.15. Deposition and website statistics for 2008, the domain annotations in 3D view, the release of the 2008 Annual Report, and the publication of a new resource for learning about PDB Data, called Looking at Structures, are described. In this quarter's Education Corner, Bernadette Uzzi talks about protein structure-related courses available from Brookhaven National Laboratory's Science Learning Center. In the Community Focus, Johannes Kirchmair and Gerhard Wolber (University of Innsbruck) discuss their paper The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery, and more.
Editions for 2008
Issue 39 - Fall 2008 (HTML |
This edition describes how Ligand Expo can be used to deposit structures, and announces the Comprehensive Format Guide for the PDB File Format (Version 3.2). Other highlights include the enhanced RSS feed for PDB structures and searches based on PubMed abstracts at the RCSB PDB website. In this quarter's Education Corner, Brad Larson (Sunset Lake Software) talks about the origin and applications of the iPhone program Molecules. In the Community Focus, Paul D. Adams (Lawrence Berkeley Laboratory) discusses PHENIX, the Technology Port of the PSI Structural Genomics Knowledgebase, and his work at the Joint BioEnergy Institute.
Issue 38 - Summer 2008 (HTML |
This edition highlights new deposition tools, such as SF-Tool and Ligand Expo, and explores usage statistics for PDB data. The New Jersey and National Protein Modeling events at the Science Olympiad are described, along with recent presentations and publications. In this quarter's Education Corner, Judy Voet (Swarthmore) and Donald Voet (University of Pennsylvania) discuss Biochemistry and Molecular Biology Education (BAMBED), a Journal for University, College, and High School Educators. John Norvell (NIGMS) discusses his career, NIGMS, and the ProteinStructure Initiative.
Issue 37 - Spring 2008
Published in HTML and PDF formats, this issue highlights deposition tools, different types of statistics about data in the PDB archive, and recent outreach activities. In the Education Corner, Jeramia Ory (Kings College) describes how he uses Chimera to create molecular multimedia in his classroom. Christine Orengo (University College London) is the subject of this quarter's Community Focus, where CATH and other research projects are described.
Issue 36 - Winter 2008
Published in a sleek new HTML format and also in PDF, this issue describes a new version of ADIT that was developed to improve data accuracy and consistency, new outreach programs, and the publication of the 2007 Annual Report. The Community Focus looks at this year's New Jersey Science Olympiad competition, and in the Education Corner, Teresa MacDonald (The University of Kansas Natural History Museum) describes edible protein models.
Editions for 2007
Issue 35 - Fall 2007
Published in HTML and PDF formats, this issue's "Message from the RCSB PDB" looks back at the many recent RCSB PDB- and wwPDB-related meetings. The newsletter also describes the "5 Easy Steps for Data Deposition with ADIT" that were presented at this past summer's ACA meeting. New features and enhancements added to the RCSB PDB website and database are reviewed. This quarter's Education Corner by Melissa Kosinski-Collins (Brandeis University) explores the Java program StarBiochem and how it can be used independently by students to view the structure and function of proteins and nucleic acids. The Community Focus interview speaks with RCSB PDB Co-Director Phil Bourne about his involvement with the computational, systems biology, and educational communities.
Issue 34 - Summer 2007
Published in HTML and PDF formats, this issue looks at the release of the remediated PDB archive, tools for depositing structures, and new features of the RCSB PDB website. This quarter's Education Corner by Alisa Zapp Machalek describes educational resources available from the NIGMS. In the Community Focus interview, Alex Wlodawer of the National Cancer Institute discusses his recent thoughts on the deposition of experimental data files, and his thoughts on reviewing macromolecular structure papers for publication in journals.
Issue 33 - Spring 2007
Published in HTML and PDF formats, Article highlights include upcoming meeting participation, deposition statistics (including experimental data) for the first quarter of 2007, and new additions to the BioSync resource. The issue also presents new features of the RCSB PDB website, including improved access to ligand data, a tool for viewing protein-ligand interactions, new advanced search options, and more. This quarter's Education Corner looks at the New Jersey Science Olympiad competition. The Community Focus interviews Angela Gronenborn, an NMR spectroscopist who is the Rosalind Franklin Professor and Chair of the Department of Structural Biology at the University of Pittsburgh.
Issue 32 - Winter 2007
Published in HTML and PDF formats, this newsletter describes new developments in data deposition and processing, including an article on how DOIs are available for released entries in the PDB archive. The issue also looks at how search results and tabular reports can be sorted, different methods for exploring protein structure domains, and how to search for sequence variants. In this quarter's Education Corner, Gary L. Gilliland reports on the X-Ray Methods in Structural Biology Course held at Cold Spring Harbor Laboratory. In the Community Focus interview, the RCSB PDB speaks with Julian Voss-Andreae, a sculptor of protein structures.
Editions for 2006
Issue 31 - Fall 2006
Published in HTML and PDF formats, this newsletter describes new developments in data deposition tools, how to use Protein Workshop to view PDB structures, and the recently added RCSB PDB Poster Prizes. In this quarter's Education Corner, Robert J. Warburton describes ways of seeing and thinking about PDB structures, and Wah Chiu discusses the future of cryo-electron microscopy in the Community Focus.
Issue 30 - Summer 2006
Published in HTML and PDF formats, this issue of the newsletter describes new developments, including pdb_extract for NMR depositions, Web Services, scripts for downloading PDB data, and the RSS feed for new structures. In this quarter's Education Corner, Cheryl Campbell describes her path to the PDB, and Michael G. Rossmann discusses his scientific career in the Community Focus.
Issue 29 - Spring 2006
Published in HTML and PDF formats, article highlights include a description of how validating structures saves overall deposition time, and a look at the online table of structures solved by multiple techniques. This quarter's Education Corner describes how the RCSB PDB was able to guide middle school students in making handheld models of the common cold. Also in this issue, Shri C. Jain describes his scientific career, from determining structures to training annotators at the RCSB PDB.
Issue 28 - Winter 2006
The Winter 2006 issue of the RCSB PDB Newsletter has been published in HTML and PDF formats. Highlights include a look at the Tools and resources at the new RCSB PDB site; Workshop for High School Teachers and Students: Building Protein Models at the Science Olympiad; a Community Focus discussion with Frank Allen, Cambridge Crystallographic Data Centre, and an Education Corner interview with Margaret A. Franzen (Pellissippi State Technical Community College, Knoxville, TN) where she discusses how her innovative classroom teaching methods focus on developing analytical thinking skills and exposing her students to the process of science. Also available in PDF format.
Editions for 2005
Issue 27 - Fall 2005
The Fall 2005 issue of the RCSB PDB Newsletter has been published in HTML and PDF formats. Highlights highlights include a look at the new site that became the main RCSB PDB site on January 1, 2006; a Community Focus discussion with William L. Duax (International Union of Crystallography and Hauptman-Woodward Medical Research Institute), and an Education Corner interview with Miriam Rossi (Vassar College) where she discusses an interdisiplinary course that familiarizes students with basic concepts of molecular structure, from an introduction to X-ray crystallographic methods through interpreting published structural papers. Also available in PDF format.
- Issue 26 - Summer 2005 Robert M. Sweet (Brookhaven National Laboratory) speaks to the RCSB PDB in this quarter's Community Focus; Gary Graper (Wisconsin Science Olympiad) describes the Protein Modeling Event for high school students; and files from the data uniformity project are released in PDBML/XML format. Also available in PDF format.
- Issue 25 - Spring 2005 Highlights from this issue include a "Community Focus" look at Stephen K. Burley (Structural GenomiX, Inc.) and an "Education Corner" story illustrating a short history of PDB structure visualization. This issue highlights additional beta site features and the pdb archive. Also available in PDF format.
- Issue 24 - Winter 2005 Highlights from this issue include a "Community Focus" look at John L. Markley (BMRB and Center for Eukaryotic Structural Genomics) and an "Education Corner" story about early protein structures painted on a wall at RCSB-Rutgers. This issue highlights some beta site features, and summarizes statistics about structures deposited to the PDB in 2004. Also available in PDF format.
Editions for 2004
- Issue 23 - Fall 2004 (HTML | PDF): Community Focus: Haruki Nakamura (PDBj); Education Corner reviews the ACA “X-ray, Molecules, and You" educational workshop
- Issue 22 - Summer 2004 (HTML | PDF): PDB_EXTRACT Integrated into CCP4 Program Suite; FASTA Sequence Files on RCSB PDB FTP Archives; Community Focus: Kim Henrick (MSD); Education Corner by J. Ricky Cox (Murray State University) on Visualization Tools
- Issue 21 - Spring 2004 (PDF): PDB Chemical Component Dictionary Format Description; Validation of Protein Structures for the PDB; Community Focus: Helen M. Berman (RCSB PDB); Education Corner by Tommie S. Hata (The Pingry School) on How the PDB, RasMol, and the Molecule of the Month are used in a high school classroom
- Issue 20 - Winter 2004 (PDF): : Announcing the Worldwide PDB; PDB_EXTRACT Makes Deposition Easier; Ligand Depot—a Small Molecule Information Resource; Searching for Experimental Data Files; Community Focus: Edward N. Baker (University of Auckland); Education Corner by Katherine Kantardjieff (California State University Fullerton) on resources for proteins, macromolecular structure/function analysis, and structural biology
Editions for 2003
- Issue 19 - Fall 2003 (PDF): Illustrations of “Macrophage and Bacterium” by Goodsell Win Award in NSF/Science Visualization Contest; Community Focus: Brian W. Matthews (University of Oregon); Education Corner by Paul A. Craig (Rochester Institute of Technology) on use of the PDB and related resources in classes at RIT
- Issue 18 - Summer 2003 (PDF): Submission of Structure Factor Data to the PDB; Community Focus with first biocurator Frances C. Bernstein; Education Corner by Tim Herman (Milwaukee School on Engineering) on Center for BioMolecular Modeling
- Issue 17 - Spring 2003 (PDF): Interview with David S. Goodsell; Gale Rhodes (University of Southern Maine) highlights education resources
- Issue 16 - Winter 2003 (PDF): PDB Highlighted on New Jersey Network News
Editions for 2002
- Issue 15 - Fall 2002 (PDF): New mmCIF and Data Processing Software; PDB CD-ROM Set #101 Released
- Issue 14 - Summer 2002 (PDF): Theoretical Model Files Moved to Separate Directory on PDB FTP Site; BioSync: A Structural Biologist’s Guide to Synchrotron Facilities
- Issue 13 - Spring 2002 (PDF): Richard E. Dickerson's 1978 equation predicts exponential growth of crystal structures; “The Art of Science”—A PDB Art Gallery Exhibit
- Issue 12 - Winter 2002 (PDF): Improved Deposition for Cryo-Electron Microscopy, Phase Out of BNL FTP Archive
Editions for 2001
- Issue 11 - Fall 2001 (PDF): Database of NIGMS Protein Structure Initiative Target Sequences; PDB Director Speaks at Research Subcommittee Hearing; PDB Chapter Published in International Tables
- Issue 10 - Summer 2001 (PDF): Prereleased Sequences Now Available; Second International Structural Genomics Meeting
- Issue 9 - Spring 2001 (PDF): New CIF Parsing Modules; Custom Reports
- Issue 8 - Winter 2001 (PDF): mmCIF Files from the Data Uniformity Project and Translation Software Released
Editions for 2000
- Issue 7 - Fall 2000 (TXT): ADIT Validation Server; NMR Task Force
- Issue 6 - Summer 2000 (TXT): Deposition Mirror Site Launched at Osaka University
- Issue 5 - Spring 2000 (TXT): RCSB PDB Celebrates its First Year of Processing Data; New Query and Reporting Features
Editions for 1999
- Issue 4 - December 1999 (TXT): Y2K availability; Completion of Layer 1 and Backlog Processing; Workshops on Structural Genomics; New Web Site for Synchrotron Users; Hand-held Models of Proteins
- Issue 3 - Fall 1999 (PDF): Transition complete; first NMR Task Force Workshop
- Issue 2 - Spring 1999 (PDF): 10,000th structure released; transition from BNL to RCSB PDB to end July 1999; description of Validation Server.
- Issue 1 - January 1999 (PDF): First issue published by RCSB PDB.
BNL Editions 1974-1999
- BNL PDB newsletters – September 1974 - February 1999: This FTP archive directory contains PDB newsletters published by Brookhaven National Laboratory.