Latest PDB News

Contents:

25-Dec-2007 Happy Holidays from the RCSB PDB
25-Dec-2007 Position Available for Senior Scientist/Scientific Software Developer
18-Dec-2007 ADITBeta Available for Testing
18-Dec-2007 Position Available for Lead Web Architect
11-Dec-2007 RCSB PDB Poster Prize Awarded at AsCA
04-Dec-2007 Announcement: Experimental Data Will Be Required for Depositions Starting February 1, 2008
27-Nov-2007 RCSB PDB Focus: Sorting Search Results
20-Nov-2007 RCSB PDB Flyers Available in Print and Online
13-Nov-2007 Web Survey: RCSB PDB Educational Resources
06-Nov-2007 New Release of pdb_extract Deposition Tool
30-Oct-2007 Southern California Wildfires and PDB Disaster Preparedness
30-Oct-2007 Fall 2007 RCSB PDB Newsletter Published
23-Oct-2007 Interview with Helen M. Berman: RCSB PDB Paper Cited More Than 5,000 Times
16-Oct-2007 Automated Downloads of PDB Data from ftp://ftp.wwpdb.org
09-Oct-2007 PDB archive at ftp://ftp.wwpdb.org
02-Oct-2007 Structure Deposition Checklist
25-Sep-2007 Art of Science exhibits in Dallas, Texas
25-Sep-2007 RCSB PDB Poster Prize Awarded at ECM
18-Sep-2007 PDB Data Summaries
11-Sep-2007 RCSB PDB Poster Prize Awarded, Art of Science shown at ISMB Meeting
04-Sep-2007 New Query and Reporting Capabilities and Features: Access to Remediation and Pre-remediation Data
28-Aug-2007 New Query and Reporting Capabilities and Features: Advanced Search
21-Aug-2007 New Query and Reporting Capabilities and Features: Improved Sequence Tabs
14-Aug-2007 New Query and Reporting Capabilities and Features: Search Result Tabs
14-Aug-2007 RCSB PDB Newsletter Summer 2007 Published
07-Aug-2007 The PDB Archive at ftp.wwpdb.org
07-Aug-2007 RCSB PDB Poster Prize Awarded at ACA Meeting
31-Jul-2007 wwPDB Remediated PDB Archive Released
24-Jul-2007 Remediated PDB Archive To Be Released on August 1, 2007
24-Jul-2007 Announcement: Data Processing Procedures
17-Jul-2007 Use the RCSB PDB Beta Website to Search and Report on Remediated Data
17-Jul-2007 ACA's Annual Meeting: Remediation Poster, Young Scientists Lecture, Exhibit Booth Demonstrations, Informatics in Structural Biology session, and Poster Prize
10-Jul-2007 Upcoming Meetings: Demonstrations, Art of Science Exhibit, and Poster Prize at ISMB
03-Jul-2007 Structural Genomics News: PSI Highlighted Structures, Technical Advances, and Assessment
26-Jun-2007 Help Desks Answer Questions about Remediated Data, the RCSB PDB Website, Deposition, and more
26-Jun-2007 Help Desks Answer Questions about Remediated Data, the RCSB PDB Website, Deposition, and more
19-Jun-2007 Exploring Ligands in the RCSB PDB Database
12-Jun-2007 Depositing NMR Structures with ADIT-NMR
05-Jun-2007 Remediated File Formats: mmCIF, PDBML-XML, and PDB
29-May-2007 Using Simple Viewer to visualize functional biological units
22-May-2007 Searching the Remediated Chemical Component Dictionary
15-May-2007 Testing Remediated PDB Files
08-May-2007 PDB Focus: First Time Depositors...
01-May-2007 RCSB PDB Newsletter Spring 2007 Published
24-Apr-2007 Announcement: Release of Remediated PDB Data
17-Apr-2007 Education Focus: DNA Day
10-Apr-2007 Using PubMed Abstracts to Search the PDB
03-Apr-2007 RCSB PDB Focus: Viewing Secondary Structure in Plain Text
27-Mar-2007 New Information and Statistics Available at BioSync
20-Mar-2007 Princeton High School Wins New Jersey Science Olympiad Protein Modeling State Finals
13-Mar-2007 RCSB PDB Focus: Saving Protein Workshop "States" for Future Visualization Sessions
06-Mar-2007 RCSB PDB Focus: Restarting ADIT depositions
27-Feb-2007 RCSB PDB Exhibit at the Biophysical Society Meeting
20-Feb-2007 Depositing and Releasing Experimental Data
13-Feb-2007 Citing Structures in the PDB: IDs, citations, and DOIs
06-Feb-2007 East Brunswick High School and Bergen County Academy Win New Jersey Science Olympiad Protein Modeling Regionals
  New Web Site Features: Advanced Search and Help Pages
30-Jan-2007 New Web Site Features For Viewing Ligand, SNP, and Pfam Data
  RCSB PDB Newsletter Winter 2007
23-Jan-2007 Time-stamped Copies of PDB Archive Available via FTP
16-Jan-2007 PDB File Formats, Annotation Procedures, and Remediation
09-Jan-2007 Browsing the PDB Using Medical Subject Headings (MeSH)
02-Jan-2007 PDB Focus: Weekly Deadlines for Release/Modify Entry Requests

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


25-December-2007

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!

Position Available for Senior Scientist/Scientific Software Developer

Available Positions with the RCSB PDB include an opening at the University of California, San Diego for a Senior Scientist/Scientific Software Developer.

18-December-2007

ADITBeta Available for Testing

A new version of ADIT, that will ensure that data in the PDB is even more accurate and consistent, is available for testing at http://deposit-beta.rcsb.org/adit/.

The RCSB PDB asks that depositors use ADITBeta to deposit their structures and provide us with any feedback at deposit@deposit.rcsb.org.

The following features have been added in this version:

This version of the tool will become the default version of ADIT early in 2008.

Position Available for Lead Web Architect

Available Positions with the RCSB PDB include an opening at the University of California, San Diego for a Lead Web Architect.

11-December-2007


AsCA poster prize winner Serah Kimani





RCSB PDB Poster Prize Awarded at AsCA

Thanks to everyone who participated in the RCSB PDB Poster Prize competition at the 8th Conference of the Asian Crystallographic Association (AsCA) from November 4-7, 2007 (Taipei, Taiwan).

The RCSB PDB Poster Prize is awarded to the best student poster related to macromolecular crystallography. At AsCA, the judges interviewed the finalists for the prize, and considered the engagement of the student in the work and their understanding of it; the clarity of the presentation in terms of the hypothesis being tested; the appropriateness of the approach; and the justification of the conclusions drawn in terms of the data presented.

The award went to Serah Kimani for "Why do nitrilases need to form helices to be active?" (Trevor Sewell, Serah Kimani (University of Cape Town), and Muhammed Sayed (University of the Western Cape, South Africa).

Judges: Mitchell Guss (University of Sydney), Sine Larsen (European Synchrotron Radiation Facility), and Mike Lawrence (Walter and Eliza Hall Institute of Medical Research).

Poster Prize Chairman: Jill Trewhella (University of Sydney)

Special thanks to the AsCA organizers and the Program Committee Chairman Se Won Suh for their assistance with organizing the prize.

Congratulations to all of the award winners in 2007.

04-December-2007

Announcement: Experimental Data Will Be Required for Depositions Starting February 1, 2008

Effective February 1, 2008, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) will be a mandatory requirement for PDB deposition.

These data must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), MSD-EBI (www.ebi.ac.uk/msd), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu).

Data can be released as soon as they have been processed and approved. There is a one-year limit on the length of time a structure and its experimental data can be put on hold, including structures that are on hold until the associated paper is published (HPUB).

This policy was developed as a result of comments and recommendations from the PDB user community, including the Commission on Biological Macromolecules of the International Union of Crystallography and the NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.

Questions relating to depositions should be sent to info@rcsb.org.


27-November-2007

RCSB PDB Focus: Sorting Search Results

Following a search that produces multiple entries, the results set can be sorted by choosing 'Sort Results' from the menu on the left hand side of the page.

For most searches, the sorting options include: PDB ID, Release Date, Residue Count, Resolution and Rank (useful with keyword searches).

An Advanced Search by sequence (Advanced Search>>Sequence Features>>Sequence (Blast/Fasta)) allows the user to sort results by PDB ID, formula weight and E value.

20-November-2007


The General Information trifold provides an overview of the RCSB PDB project





RCSB PDB Flyers Available in Print and Online

The News & Publications page offers links to various RCSB PDB publications, including newsletters, annual reports, and brochures.

These informational brochures describe different RCSB PDB features, including the Sea of Genes exhibit at the Birch Aquarium (Scripps) that explores proteins related to underwater creatures.

5 Easy Steps for Structure Deposition describes the tools that facilitate NMR and X-ray crystal structure deposition and validation for use by the authors of the structures.

A General Information trifold provides an overview of the RCSB PDB project, and includes information about data deposition, data query and reporting, Molecule of the Month, structural genomics, wwPDB, and outreach and education resources.

All of these materials can be downloaded from the RCSB PDB site. To receive printed copies of these flyers, please send your postal address and brochure request to info@rcsb.org. Requests can be made for multiple copies.

If you are interested in receiving the upcoming 2007 Annual Report, or would like to subscribe to our quarterly newsletter, please send your postal address to info@rcsb.org.

13-November-2007

Web Survey: RCSB PDB Educational Resources

The RCSB PDB is looking for feedback about the educational resources available from our website. We would also like to know the types of educational activities and resources that are of interest to our users.

We've created a short online survey that should only take a few minutes to answer.

We greatly appreciate your participation in this survey. As a token of appreciation, we'll send temporary tattoos of tRNA to survey respondents who send their postal address to info@rcsb.org.

06-November-2007

New Release of pdb_extract Deposition Tool

pdb_extract is a program that minimizes errors and saves time during the deposition process by extracting key details from the output files produced by many X-ray crystallographic and NMR applications for use in the deposition process. 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.

Version V3.004 of pdb_extract has been released, and provides:

Complete details are available in the release notes at http://sw-tools.rcsb.org/apps/PDB_EXTRACT/latestrelease-v3.004.html.

pdb_extract can be used via web interface or downloadable workstation from pdb-extract.rcsb.org.

30-October-2007

Southern California Wildfires and PDB Disaster Preparedness

As many of you know, extensive wildfires caused widespread destruction throughout much of Southern California. More than 500,000 people were evacuated in San Diego County, including many RCSB PDB staff members. The RCSB PDB website (www.pdb.org) and the PDB FTP archive (ftp.wwpdb.org) are hosted at the San Diego Supercomputer Center (www.sdsc.edu) on the University of California, San Diego (www.ucsd.edu) campus. Essential PDB operations continued uninterrupted at the height of the firestorms, including the weekly update on Tuesday, October 23, thanks to the RCSB PDB staff, the dedication of many people at UCSD, and the power of the Internet.

Failover sites are maintained at the Skaggs School of Pharmacy and Pharmaceutical Sciences (pharmacy.ucsd.edu), also on the UCSD campus; and at Rutgers, the State University of New Jersey (www.rutgers.edu). Availability of services at the primary site, and, if necessary, transfer of services to the failover sites, are automatically monitored and enacted by an outside DNS service. The PDB archive is also mirrored by wwPDB members MSD-EBI and PDBj.

The RCSB PDB continues to review and enhance its plans for disaster preparedness and recovery. Questions and comments may be sent to info@rcsb.org.

Quarterly Newsletter

Fall 2007 RCSB PDB Newsletter Published

The latest RCSB PDB Newsletter has been published in HTML and PDF formats.

This issue's "Message from the RCSB PDB" looks back at the many different RCSB PDB- and wwPDB-related meetings held this past September. The newsletter also describes the "5 Easy Steps for Data Deposition with ADIT" that were presented at this past summer's ACA meeting.

The 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.

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

Subscription information for the plain text electronic version is also available.

23-October-2007

Interview with Helen M. Berman: RCSB PDB Paper Cited More Than 5,000 Times

According to Essential Science IndicatorsSM, the primary reference for the RCSB PDB is ranked #4 in the top cited Biology and Biochemistry papers of the past ten years. "The Protein Data Bank", published in the 2000 Database Issue of Nucleic Acids Research, has been cited more than 5,000 times.

Director Helen M. Berman discusses this paper in an interview with in-cites magazine at www.in-cites.com/papers/HelenBerman.html.

16-October-2007

Automated Downloads of PDB Data from ftp://ftp.wwpdb.org

The PDB archive at ftp://ftp.wwpdb.org provides coordinate data (in PDB, mmCIF, and PDBML/XML formats) and experimental data. New features and improved query functionality on the RCSB PDB website reflect the data enhancements that resulted from the wwPDB Remediation Project.

A web interface offers a way to download multiple data files from the archive.

Scripts are also available to assist in the automated download of data from the ftp site:

Additional information is available from ftp://ftp.wwpdb.org/pub/pdb/README about:

Questions and comments about downloading data should be sent to info@rcsb.org.

09-October-2007

PDB archive at ftp://ftp.wwpdb.org

As previously announced, the PDB archive has been moved to ftp://ftp.wwpdb.org. Updated weekly, this location serves the files from the wwPDB Remediation Project and all newly released files. In September, approximately 14.7 million files were downloaded from ftp.wwpdb.org.

During the same period, 2.7 million files were downloaded from the snapshot of unremediated data at ftp.rcsb.org. This site is no longer being updated.

Users are strongly encouraged to update any automatic scripts or bookmarks to ftp://ftp.wwpdb.org.

The transition to ftp://ftp.wwpdb.org was designed so that users' private copies of the ftp archive would not be overwritten. Reminders about this transition have been sent to depositors and help desk correspondents. In some cases, users performing bulk downloads from the old site were contacted individually.

The RCSB Protein Data Bank would like to thank its users for their attention and cooperation during this transition. Questions and comments should be sent to info@rcsb.org.

02-October-2007

Structure Deposition Checklist

It is recommended to have the following items on hand when depositing a structure:

More detailed checklists specific to X-ray, NMR, and electron microscopy (EM) depositions are available at:

Questions about this news item should be sent to info@rcsb.org.




Virus Capsid by Julian Voss-Andreae (2003, Cast and fabricated bronze, length 9") The Art of Science exhibit features images available from the RCSB PDB website and the Molecule of the Month. Also included are pieces from the protein sculptor Julian Voss-Andreae, including this sculpture of a piece of a virus shell.





25-September-2007

Art of Science exhibits in Dallas, Texas

Images from the RCSB PDB's Art of Science exhibit are now on display at The University of Texas Southwestern Medical Center in Dallas, Texas, sponsored by the Molecular Biophysics Graduate Program. The exhibit, which will be on view on the 8th Floor of the T. Boone Pickens Biomedical Building, opened on September 25, 2007 in conjunction with the Molecular Biophysics' "Meet the Program" Poster Presentations. The show will run until October 5th.

Questions about this news item should be sent to info@rcsb.org.






RCSB PDB Poster Prize Awarded at ECM

Thanks to everyone who participated in the recent RCSB PDB Poster Prize competition for best student poster related to macromolecular crystallography at the 24th European Crystallographic Meeting held in Marrakech August 22-27, 2007.

The award went to Humberto Couto Fernandes for "Yellow lupine pathogenesis-related protein as a reservoir for cytokinins" (Humberto Fernandes, Anna Bujacz, Oliwia Pasternak, Grzegorz Bujacz, Michal Sikorski, Mariusz Jaskólski, Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland).

Judges: Alexander Wlodawer (National Cancer Institute at Frederick), Wolfram Saenger (Freie Universitaet Berlin), Vilmos Fulop (University of Warwick), Tomitake Tsukihara (Osaka University)

Poster Prize Chairman: Anders Liljas (Lund University)

Special thanks to John Helliwell and Petra Bombicz for their help with organizing this prize.

18-September-2007

PDB Data Summaries

Various summaries of current data in the PDB archive are available through the /pub/pdb/derived_data directory on the FTP site at ftp://ftp.wwpdb.org as well as the summaries page on the RCSB PDB web site. Summaries include:

Questions about these files should be sent to info@rcsb.org.

11-September-2007


The Art of Science exhibit was part of the ISMB meeting. Special thanks to the ISMB's Steven Leard, BJ Morrison, and Burkhard Rost for their support and help with the exhibit and the poster prize.

RCSB PDB Poster Prize Awarded, Art of Science shown at ISMB Meeting

Thanks to everyone who participated in the recent RCSB PDB Poster Prize competition for best student poster related to macromolecular crystallography at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB) held in Vienna, Austria July 21-25, 2007.

The award went to Keren Lasker for "Determining the configuration of macromolecular assembly components based on cryoEM density fitting and pairwise geometric complementarity" (Keren Lasker, Tel Aviv University and University of California, San Francisco; Maya Topf, Birkbeck College, University of London; Andrej Sali, University of California, San Francisco; Haim Wolfson, Tel Aviv University).

Judges: Yanay Ofran (Columbia University), Predrag Radivojac (Indiana University), Alejandro Giorgetti (University of Rome), Riccardo Percudani (Universit? di Parma), Michael Tress (Spanish National Cancer Research Centre), and Sean Mooney (Indiana University School of Medicine).

Poster Prize Chairman: Marco Punta (University of Georgia)

04-September-2007

New Query and Reporting Capabilities and Features: Access to Remediation and Pre-remediation Data

All data in the PDB archive ( ftp://ftp.wwpdb.org) reflects the new features incorporated as part of the wwPDB Remediation Project, including standardized IUPAC nomenclature for chemical components. These data have been incorporated into the RCSB PDB website and database to provide improved searching and reporting capabilities. Access to the unremediated data is possible for individual structures and for the entire archive.

The left menu of each Structure Summary page provides download options for either remediated or unremediated data in a variety of formats. The Remediation Tab will appear on this page to describe any changes to chain and residue naming conventions made to make the archive more consistent. An example description would be "This structure's single unnamed chain was assigned chain id A".

A snapshot of the entire unremediated PDB archive (as of July 31, 2007) is available at ftp.rcsb.org.

28-August-2007

New Query and Reporting Capabilities and Features: Advanced Search

The data in the PDB archive offers a wealth of valuable metadata. Advanced Search is a powerful and easy-to-use interface to the underlying search architecture and remediated data. Complex queries are constructed by combining simple "subqueries" chosen from a drop-down list. Users get a feel for the likely success of their search strategy while constructing the search by checking the number of results for each subquery.


An example of an advanced search which combines searches by keyword, sequence motif, and resolution. Additional queries can be added.

A broad range of subqueries is available including sequence searches; GO assignments; SCOP and CATH domain assignments; and author name searches.

These subqueries may be combined into a complex query by searching "all" or "any" of the user-specified subqueries.

Advanced Search is accessible from the Search Tab in the left menu or from the search bar at the top of this page.

Click here for a flash tutorial on how to use the advanced search tool.

21-August-2007

New Query and Reporting Capabilities and Features: Improved Sequence Tabs

The Sequence Details tab offers a customizable report that displays polymer chain sequences annotated with properties such as domain and secondary structure. This feature utilizes data from the Remediation Project to provide an exact mapping of the structure sequence to the UniProt 1 sequence. Annotations from CATH, 2 DSSP, 3 PDP, 4 and the author-approved secondary structure can be applied to either the sequence in UniProt or in the PDB entry's SEQRES information.

The size of the report can be customized for use in presentations.


The first 60 residues of T4 lysozyme (108l) are mapped to their entries in CATH, DSSP, and UniProt.
Mutations in the sequence are shown in red.

1 (2007) The Universal Protein Resource (UniProt). Nucleic Acids Res. 35(Database issue): D193-7.

2 C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton (1997) CATH- a hierarchic classification of protein domain structures. Structure. 5: 1093-1108.

3 W. Kabsch and C. Sander (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22: 2577-2637.

4 N. Alexandrov and I. Shindyalov (2003) PDP: protein domain parser. Bioinformatics. 19(3): 429-30.

14-August-2007

New Query and Reporting Capabilities and Features: Search Result Tabs

Since the RCSB PDB website utilizes the data from the wwPDB Remediation Project, queries will now return a more accurate set of results.

Keyword or Advanced Searches will also return different ways of exploring the search results list. Options available from the tabs shown above the default results list include:

* The Gene Ontology Consortium (2000) Nature Genetics 25:25-29; Conte, L., Bart, A., Hubbard, T., Brenner, S., Murzin, A. & Chothia, C. (2000) Nucleic Acids Res. 28: 257-259; Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997) Structure 5:1093-1108.


RCSB PDB Newsletter Summer 2007 Published

The latest RCSB PDB Newsletter has been published in HTML and PDF formats

This newsletter describes the recent 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.

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

Subscription information for the plain text electronic version is also available.

07-August-2007

The PDB Archive at ftp.wwpdb.org

Data annotated and released by members of the wwPDB are available for download from ftp.wwpdb.org. This site is updated on a weekly basis.

All data in the PDB archive reflects the new features incorporated as part of this wwPDB project, including standardized IUPAC nomenclature for chemical components. Users may have to download new software to view the files with the new nomenclature (e.g., RasMol, Chimera) or update their scripts for automatic downloads. Please see remediation.wwpdb.org for details.

A snapshot of the unremediated PDB archive (as of July 31, 2007) will be available at ftp://ftp.rcsb.org. This site has been frozen, and will not be updated.

RCSB PDB Poster Prize Awarded at ACA Meeting

Thanks to everyone who participated in the recent RCSB PDB Poster Prize competition for best student poster related to macromolecular crystallography at the ACA.

Hasan Demirci for "Structure Based Protein Enginering of Ribosomal Protein Trimethyltransferase" (Hasan Demirci, Steven T. Gregory, Albert E. Dahlberg, Gerwald Jogl. Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University).

The award at the American Crystallographic Association's Annual Meeting (July 21-26; Salt Lake City, UT) went to Hasan Demirci for "Structure Based Protein Enginering of Ribosomal Protein Trimethyltransferase" (Hasan Demirci, Steven T. Gregory, Albert E. Dahlberg, Gerwald Jogl. Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University).

Judges: Mitchell J. Guss (University of Sydney), Peter Horanyi (University of Virginia), Thomas Koetzle (Argonne National Laboratory), James Phillips (Duke University Medical Center), Bernard Santarsiero (University of Illinois at Chicago), and Timothy Umland (Hauptman-Woodward Medical Research Institute)

Poster Prize Chairman: John Rose (University of Georgia)

31-July-2007

wwPDB Remediated PDB Archive Released

The PDB archive that has been remediated by the wwPDB is available from ftp.wwpdb.org. Searches and reports performed on the RCSB PDB website will now utilize these data.

The FAQ below answers general questions about the remediation project and technical questions downloading the data files.

wwPDB Remediation Project: Frequently Asked Questions

General Questions

Technical Questions

This document is also available as a PDF from www.wwpdb.org/docs.html.

24-July-2007

Remediated PDB Archive To Be Released on August 1, 2007

The PDB archive has been remediated and will be available starting August 1, 2007 from ftp.wwpdb.org. All data in the PDB archive will reflect the new features incorporated as part of this wwPDB project, including standardized IUPAC nomenclature for chemical components.

Users may have to download new software to view the files with the new nomenclature (e.g., RasMol, Chimera). Please see http://remediation.wwpdb.org/software.html for details.

A snapshot of the unremediated PDB archive (as of July 31, 2007) will be available at ftp://ftp.rcsb.org.

An FAQ about this project and transition is available at www.wwpdb.org/docs.html.

Questions about any of these events should be sent to info@rcsb.org

Announcement: Data Processing Procedures

Starting August 1, 2007, files processed and released into the archive by the wwPDB sites will reflect the new features incorporated as part of the remediation project. These files will follow the PDB Exchange Dictionary (PDBx) v1.045 and the Protein Data Bank Contents Guide Version 3.1.

There is no change to how depositors submit their files. Any required changes in nomenclature can be made automatically by the wwPDB during the annotation process.

For more information, please see www.wwpdb.org.

Questions about any of these events should be sent to info@rcsb.org

17-July-2007

Use the RCSB PDB Beta Website to Search and Report on Remediated Data

The RCSB PDB website that utilizes the data from the wwPDB Remediation Project is available at betastaging.rcsb.org. It will become the production site at www.pdb.org after a period of testing.

This site offers:

Questions about any of these events should be sent to info@rcsb.org

ACA's Annual Meeting: Remediation Poster, Young Scientists Lecture, Exhibit Booth Demonstrations, Informatics in Structural Biology session, and Poster Prize

The RCSB PDB will be actively involved with the Annual National Meeting of the American Crystallographic Association (ACA) July 21-26, 2007 in Salt Lake City, UT.

Questions about any of these events should be sent to info@rcsb.org

10-July-2007

Upcoming Meetings: Demonstrations, Art of Science Exhibit, and Poster Prize at ISMB

The RCSB PDB will be involved in several activities at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB) that will be held in Vienna, Austria from July 21-25, 2007.

Questions about any of these events should be sent to info@rcsb.org

03-July-2007

Featured as a June 2007 PSI Structure of the Month, this NMR solution structure of a plant protein may function in host defense. This protein was expressed in a convenient and efficient wheat germ cell-free system. Credit: Center for Eukaryotic Structural Genomics

Structural Genomics News: PSI Highlighted Structures, Technical Advances, and Assessment

The RCSB PDB Structural Genomics Information Portal offers online tools, summary reports, and target information related to structural genomics. This site also links to new features from the Protein Structure Initiative (PSI). The PSI Structures of the Month highlights recent structures solved by the current centers, while the PSI Technical Highlights describes methods developed by researchers to streamline the structure determination process. These features include links to related information, such as PDB structure summaries, published papers, and center Web sites.

To date, the overall PSI effort has resulted in nearly 2,500 structures of which 70 percent share less than 30 percent of their sequence with known proteins. Methods and tools developed during the first phase of the PSI have been incorporated into the centers' structural genomics pipelines and adopted by structural biology labs worldwide.

The National Institute of General Medical Sciences, which supports the PSI, currently is engaged in an assessment of the project and invites scientists, scientific organizations, and other interested parties to participate in this assessment by July 20, 2007. A formal Request for Information has been posted in the NIH Guide for Grants and Contracts.

26-June-2007

Help Desks Answer Questions about Remediated Data, the RCSB PDB Website, Deposition, and more

Electronic help desks are available to support users exploring PDB data.

info@wwpdb.org is available to address questions regarding the remediated PDB archive. The wwPDB appreciates the feedback from users who have examined the Chemical Component Dictionary and files in the remediated archive. Further information about this project is available at www.wwpdb.org.

deposit@deposit.rcsb.org answers questions about the deposition and annotation process at the RCSB PDB.

Support pages at deposit.pdb.org include a file deposition and release FAQ, an overview of software tools, and tutorials for using ADIT, pdb_extract, the Validation Server, and Ligand Depot.

info@rcsb.org responds to requests relating to the navigation of the RCSB PDB website. Questions about searching, reporting, and using all of the resources available from the RCSB PDB should be sent to this address.

The RCSB PDB help system launches a separate browser window to allow users to access the help information and the website at the same time. It offers detailed topics (including Getting Started, Download Files, Search/Browse the Database, and Results), an index, glossary, and search engine.


back to top

19-June-2007

Exploring Ligands in the RCSB PDB Database

(Click image to enlarge)
The Advanced Search for Ligands

A ligand name can be entered in the keyword text search at the top of any page from the RCSB PDB website. The Advanced Search query engine can also be used to search for structures based upon ligands — based upon the ligand's name, ID code, or SMILES string.

In addition to reviewing the structures that match the given query constraints, users can select the 'Ligand Hits' tab, which lists the ligands known to interact with the structures matching the query. The Ligand Hits tab also offers a gallery view of ligand images.

Selecting one of the ligands from the this tab returns a summary page with chemical and structural details. The page offers interactive and static views of the ligand. Users may also download 'model' coordinates (the experimental coordinates from the first deposition of the ligand) and 'ideal coordinates' (generated from the model coordinates and their connectivity) in a variety of formats including CIF, XML, SDF and PDB.

The PDB chemical components dictionary (formally the HET dictionary) containing these ligands has been remediated to better describe the components that interact with macromolecular structures. Please go to wwpdb.org to learn more about this remediation project, and the release of the archive of remediated data files.

More information about ligand searching and viewing is available.


back to top

12-June-2007

Depositing NMR Structures with ADIT-NMR

Users can now deposit NMR structure and experimental data using one tool: ADIT-NMR. Available from batfish.bmrb.wisc.edu/bmrb-adit, ADIT-NMR can be used to precheck, validate, and deposit NMR structures. Coordinates and constraint data will be processed and released by the RCSB PDB, while other NMR spectral data (such as chemical shifts, coupling constants, and relaxation parameters, etc.) will be processed and archived by BMRB.

All new NMR depositions at RCSB PDB will be submitted using ADIT-NMR. The assignment of PDB/BMRB IDs and the movement of data files between sites is fully automated. More than 100 joint depositions have already been processed through this new system. Any unfinished NMR deposition sessions that were started using ADIT before May 16, 2007 will continue to be available at that site.

Other tools for NMR depositions include:

back to top

05-June-2007

Remediated File Formats: mmCIF, PDBML-XML, and PDB

The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files. The remediated data files are currently available for testing before they become the main PDB archive in three formats:

The entire PDB archive has been reviewed and remediated by the wwPDB with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

Questions and comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website as well as on the individual member websites.


back to top

29-May-2007

Using Simple Viewer to visualize functional biological units


(Click image to enlarge)
The biological unit of 1AEW in Simple Viewer

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. For many of these structures, the asymmetric unit represents the functional biological molecule. In other cases, the biological unit can be generated from the asymmetric unit.

In these cases, Protein Workshop can be used to display the asymmetric unit and Simple Viewer can be used to explore the functional biological unit of a structure. Simple Viewer can rotate a structure, zoom in and out, and then save the view of the biological unit as an image file.

Simple Viewer tool can be launched from the "Display Options" found on an entry's Structure Summary page. Simple Viewer requires Java version 1.4 or greater.

Citation information is available for images created using Simple Viewer.

An Introduction to Biological Units and the PDB Archive is available to describe asymmetric and biological units in more detail.


The biological unit of 1AEW.

The asymmetric unit of 1AEW.
back to top

22-May-2007

Searching the Remediated Chemical Component Dictionary

The Chemical Component Dictionary has been remediated to address the inconsistencies in older dictionary entries that resulted in valence problems, missing model coordinates, and redundant ligands.

The features of the new dictionary include:

The full Chemical Component Dictionary and the companion Amino Acid Variants Dictionary can be downloaded from http://remediation.wwpdb.org/downloads.html.

Users can also search for individual chemical components, either by entering the component ID in the form provided, or by browsing by ID. The variant dictionary can also be browsed.

This dictionary was remediated as part of the wwPDB's Remediaton Project. In addition to the improvements made as a result of the Chemical Component Dictionary, this project reviewed the PDB archive and updated sequence database references and taxonomies; resolved any remaining differences between chemical and macromolecular sequences; improved the representation of viruses; and verified primary citation assignments.

The remediated data files are currently available for testing before they become the main PDB archive. Questions and comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website as well as on the individual member websites.

back to top

15-May-2007

Testing Remediated PDB Files

The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files.

These files are available for community testing in a variety of ways, including:

The entire PDB archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

Questions or comments about the remediation project should be sent to info@wwpdb.org.

back to top

08-May-2007

PDB Focus: First Time Depositors...

There are a few steps a depositor can take to make the process of depositing a structure to the PDB quick, easy, and accurate! This is an iterative process. If you encounter problems at a particular step, please make the correction(s) and go through the steps again.

  1. Use the pdb_extract Program Suite to extract information needed for deposition from output files produced by many structure determination applications.
  2. Check your structure with the Validation Suite and Server to ensure that the data being deposited are accurate and reflect what you intend to submit.
  3. Run BLAST (at NCBI) to compare your sequence to sequence database references. Any necessary corrections can then be made to your sequence and coordinates.
  4. Use Ligand Depot to find the proper 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@deposit.rcsb.org.
  5. Deposit your structure using ADIT, using its editor to add any missing information to the deposition.

For a detailed packet of information about first-time deposition, including reprints about validation and Ligand Depot, please send your postal address to info@rcsb.orgwith the subject line "first time depositor packet".

back to top

01-May-2007


RCSB PDB Newsletter Spring 2007 Published

The latest RCSB PDB Newsletter has been published in HTML and PDF formats.

This newsletter describes 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 and the winners of the protein modeling trial event that was sponsored and judged by the RCSB PDB.

In the Community Focus interview, the RCSB PDB speaks with Angela Gronenborn, an NMR spectroscopist who is the Rosalind Franklin Professor and Chair of the recently established Department of Structural Biology at the University of Pittsburgh.

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

Subscription information for the plain text electronic version is also available.

back to top

24-April-2007

Announcement: Release of Remediated PDB Data

The wwPDB has collaborated on a project to remediate the PDB archive and create a new set of corrected files.

A new FTP server containing the remediated data has been set up for testing. The access details for this site are provided at http://www.wwpdb.org/remediation-downloads.html. The new ftp site will be updated weekly in concert with current production site at ftp://ftp.rcsb.org. Both sites share the same organizational structure.

The entire archive has been reviewed and remediated with the objectives of improving the detailed chemical description of non-polymer and monomer chemical components; standardizing atom nomenclature; updating sequence database references and taxonomies; resolving any remaining differences between chemical and macromolecular sequences; improving the representation of viruses; and verifying primary citation assignments. In addition, the atom nomenclature for amino acids and nucleotides now conforms with IUPAC standards.

Your input is very important to us. PDB users are encouraged to test the remediated data files between April and July 2007. The details of the final transition will be announced on this website.

Detailed information about this project can be found at http://remediation.wwpdb.org.

Comments about the files should be sent to info@wwpdb.org. Major announcements will be made at the wwPDB website ( http://www.wwpdb.org) as well as on the individual member websites.

 

back to top

 

17-April-2007

Education Focus: DNA Day

"National DNA Day" will be celebrated on April 25. Commemorating the completion of the Human Genome Project in April 2003 and the discovery of DNA's double helix.

DNA Day encourages teachers and students to celebrate these historic achievements. Online resources relating to DNA Day include the following:


Ethan Quanci, Alex Romash, and Sam Silver with their model of DNA

Dr. Judith McGonigal's 8th grade class created a 3D model of DNA out of swimming pool "noodles". Haddonfield, NJ middle schooler Ethan Quanci (left) liked the scale of the model, because "as we all know whenever you need to comprehend the process of something small and complex ... make it BIG."

Alex Romash (middle) felt that "During the process of creating our molecule I felt just like I was part of Crick and Watson's team and that we were creating history just like they did." Sam Silver is on the right. To build your own DNA model, try Science in School's lesson on Modelling the DNA double helix using recycled materials.

 

back to top

 

10-April-2007

Using PubMed Abstracts to Search the PDB


(Click image to enlarge) The Abstract link is circled

PubMed abstracts are accessible from a published entry's Structure Summary page. The "Abstract" link returns a page with the article title, abstract, keywords, authors, organizational affiliation, journal, and PubMed identifier. The PubMed abstract at NCBI can also be viewed by clicking on the icon next to "Abstract".


(Click image to enlarge)

Clicking on the "KIX" in the abstract enters it in the search box

The text box at the bottom of the Abstract page can be used to search for related 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.

 

back to top

 

03-April-2007

RCSB PDB Focus: Viewing Secondary Structure in Plain Text


(Click image to enlarge)

Clicking on the page icon (circled) brings the user to a textual display of secondary structure.



(Click image to enlarge)

Sequence and secondary structure for chain A of 2OKJ
(Fenalti, G., Law, R.H.P., Buckle, A.M., Langendorf, C., Tuck, K., Rosado, C.J., Faux, N.G., Mahmood, K., Hampe, C.S., Banga, P., Wilce, M., Schmidberger, J., Rossjohn, J., El-Kabbani, O., Pike, R.N., Smith, A.I., Mackay, I.R., Rowley, M.J., Whisstock, J.C. GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop Nat.Struct.Mol.Biol. (2007) doi:10.1038/nsmb1228)

For any released structure, the 'Sequence Details' tab offers summary information related to sequence. On this page, the sequence and secondary structure table uses graphics to illustrate secondary structure and domain information.

A textual display of secondary structure is linked from the little 'page' icon at the top right (in the dark gray bar).

The sequence and its corresponding secondary structure information is shown in paired lines. The first line in a pair provides the amino acid sequence, colored red for helices, blue for beta strands and bridges, and green for turns and bends. The line underneath indicates the secondary structure using the abbreviations from Kabsch and Sander shown below.

Letter Secondary Structure

† Reference:
   Kabsch, W. and Sander, C. (1983) Biopolymers 22:2577-2637.

 

back to top

 

27-March-2007

New Information and Statistics Available at BioSync


BioSync

The BioSync website now contains updated beamline descriptions for operational US synchrotron beamlines as well as some basic information for almost all operational international beamlines.

PDB deposition statistics, grouped by site and beamline, can be found at biosync.rcsb.org. Galleries of structures, also grouped by site and beamline, are cross-linked to structure summary pages in the RCSB PDB. Tables of primary citations and some general information (phasing software, resolution, R-factors, etc.) are also provided. Most recently, similar tables and galleries have been added for structural genomics structures solved from synchrotron data.

BioSync (Structural Biology Synchrotron Users Organization) was formed in 1990 as a grassroots organization intended to promote access to synchrotron radiation. The BioSync resource, originally designed and hosted by UCSD/SDSC, has been updated and is now being maintained by the RCSB PDB.

Updates to beamline descriptions from local personnel as well as general comments and suggestions are most welcome at BioSync@rcsb.rutgers.edu .

 

back to top

 

20-March-2007


Ola Hadaya, Sarah Goodman, and Yong Kim from Princeton High School

Princeton High School Wins New Jersey Science Olympiad Protein Modeling State Finals

At the NJ Science Olympiad (NJSO) State Finals, teams from all over the garden state presented their hand-built 3D models of a major histocompatibility complex (MHC) protein, along with an abstract, to be judged by annotators from the RCSB PDB. After taking a written exam about MHC and protein structure and function, the highest ranking teams were Princeton High School (First Place), Montgomery High School (Second), and The Lawrenceville School (Third).

Congratulations to all of the teams who participated in this trial event -- there were many great models, abstracts, and responses to the exam. Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to buildmodels@deposit.rcsb.org.


RCSB PDB annotators judged the models, abstracts, and written exams

Special thanks to our judges from the RCSB PDB (Shuchismita Dutta, Irina Persikova, Monica Sekharan, and Christine Zardecki (Event Supervisor)), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

 

back to top

 

13-March-2007


(Click image to enlarge)

A section of MHC as viewed in Protein Workshop. PDB ID: 1hsa. D.R. Madden, J.C. Gorga, J.L. Strominger, D.C. Wiley. (1992) The three-dimensional structure of HLA-B27 at 2.1 Angstrom resolution suggests a general mechanism for tight peptide binding to MHC. Cell 70:1035-1048.

RCSB PDB Focus: Saving Protein Workshop "States" for Future Visualization Sessions

Protein Workshop is a molecular viewer accessible from every PDB entry's Structure Summary page. Its simple interface lets users quickly and easily select structural elements and change the coloring, labeling, and representation style (ribbons, cylinders, and more). Users can also color specific structural features such as conformation type and hydrophobicity.

Protein Workshop is an excellent tool for generating high-resolution images in JPG, BMP, TIFF, WBMP, and PNG formats. A tutorial for creating these images is available.

This tool offers a way to save the "state" of a Protein Workshop session. Users can rotate and zoom a structure to a particular orientation and then capture this view for later use. To save a state, enter a title next to the "Capture current viewer state" from the Options menu, and then select the adjacent button. The name of this state will be listed in the box below. The view of the molecule can then be changed around, but users can always go back to saved states by clicking on the state's name.

These states can be saved in a XML file for later use by selecting the state and clicking the "Export selected state" button. States can be restored from a file by clicking the "Import state" button.

This tool uses the Molecular Biology Toolkit (mbt) and JOGL technology, and requires no installation other than the most recent version of Java. A tutorial is provided to guide users in using Protein Workshop.

Figures created using Protein Workshop should cite the RCSB PDB and the mbt.

 

back to top

 

06-March-2007

RCSB PDB Focus: Restarting ADIT depositions

A structure can be deposited in more than one Internet session by using ADIT's "Session Restart ID" feature. This identifier appears in red in the center of the browser window when ADIT's "deposit" step is first started. It is also seen in the title of the browser throughout the deposition session.

The case-sensitive restart ID should be entered in the space provided on the ADIT home page to return to the undeposited entry. Any data entered in a category are stored every time the user selects the SAVE button. All entered data associated with a particular entry can be accessed using the restart ID until the "DEPOSIT NOW" button is selected, for up to six months after the session has been last updated.

ADIT is available at the RCSB PDB and PDBj. ADIT-NMR can be used to deposit data to the PDB and BMRB in one session.

A tutorial guide to using ADIT is available in English and Japanese. Example "in progress" deposition sessions are available to practice learning how to use ADIT at http://rcsb-deposit-demo-1.rutgers.edu.

 

back to top

 

27-February-2007

RCSB PDB Exhibit at the Biophysical Society Meeting



Stop by the RCSB PDB exhibit booth to meet with RCSB PDB members and for related materials: tutorials, flyers, and temporary tattoos!

The RCSB PDB will participate in the exhibition at the 51st Annual Meeting of the Biophysical Society (March 3-7 in Baltimore, Maryland). Staff will be available at booth #639 to answer questions and to demonstrate the deposition and query features available from www.pdb.org. We hope to see you there!

 

back to top

 

20-February-2007

Depositing and Releasing Experimental Data

The RCSB PDB strongly encourages depositors to follow the guidelines set by the IUCr, the NIH, and the journals regarding the submission and release of coordinate and experimental data.

Deposition of experimental data (structure factor and/or NMR constraint files) is required by many journals, including Acta Crystallographica, Biochemistry, Cell, Nature, and Science.

These files can be uploaded during the ADIT deposition process.

Depending upon the hold status selected by the depositior, data release can occur when a depositor gives approval (REL), the hold date has expired (HOLD), or the journal article has been published (HPUB). There is a one-year limit on the length of a hold period, including HPUBs. If the citation for a structure is not published within the one-year period, depositors will be given the option to either release or withdraw the deposition.

Detailed deposition and release information is available from http://deposit.pdb.org/.

 

back to top

 

13-February-2007

Citing Structures in the PDB: IDs, citations, and DOIs

The contents of the PDB are in the public domain. Structures can be cited using their PDB ID and the published citation related to the structure.

Detailed information for citing the use of data, structures (with examples), and images is available.

 

back to top

 

06-February-2007

East Brunswick High School and Bergen County Academy Win New Jersey Science Olympiad Protein Modeling Regionals


Leebyn Chong and Anthony Sin of East Brunswick High School

Several high school teams competed in the protein modeling trial events at the New Jersey State Science Olympiads held January 9 (Central Regional) and 11 (Northern Regional). Each team created a three-dimensional model of an insulin structure, accompanied by a written description, using resources available from the RCSB PDB. At the event, teams also answered multiple choice and short answer-questions focusing on the structure and function of insulin. The three-dimensional protein models are built using Mini-Toober kits provided by the RCSB PDB.


Marina Mainescu, Benjamin Yang, and Edward Hong of Bergen County Academy

At the Central Regional, East Brunswick High School (First Place and the 2006 State Champions in this event), West Windsor-Plainsboro South HS (Second), and West Windsor-Plainsboro North HS (Third) created very strong models.

At the Northern Regional, Bergen County Academy (First Place), Westfield HS (Second), and New Providence HS (Third) exhibited very strong skills.


Annotators carefully examined all of the models

Special thanks to our judges from the RCSB PDB (Shuchismita Dutta, Irina Persikova, Massy Rajabzadeh, Monica Sekharan, Jasmine Young, Muhammed Yousufuddin, and Christine Zardecki (Event Supervisor)), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event. We look forward to seeing everyone at the state competition on March!

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

 

back to top

 

New Web Site Features: Advanced Search and Help Pages


(Click image to enlarge)

The MeSH browser





(Click image to enlarge)

Some of the many Advanced Search options

In addition to new features such as improved access to ligand, SNP, and Pfam information, new options have also been added to the Advanced Search and help features.

Please write to info@rcsb.org with any questions or comments about these new features.

 

back to top

 

30-January-2007

New Web Site Features For Viewing Ligand, SNP, and Pfam Data


The Ligand Hits tab from a search for 'protein kinase'


The Ligand Summary page offers summary information, downloads (definitions and coordinates), and interactive and static views. HEM is shown here.


A look in Ligand Explorer at a hydrophobic binding pocket for ATP in entry 1ATP. To access Ligand Explorer, click the 'View' button under 'Ligand Interaction' on the Structure Summary page.

The RCSB PDB website now offers improved access to ligand, Single Nucleotide Polymorphism (SNP), and Pfam information.

 

back to top

 


RCSB PDB Newsletter Winter 2007

The latest RCSB PDB Newsletter has been 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.

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

Subscription information for the plain text electronic version is also available.

back to top

23-January-2007

Time-stamped Copies of PDB Archive Available via FTP

A time-stamped snapshot of the PDB archive as of January 2, 2007 has been added alongside time-stamped copies of the archive from January 2006 and 2005 at ftp://snapshots.rcsb.org/. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

The directory 20070102 includes the 40,933 experimentally-determined coordinate files that were current (i.e., not obsolete) as of January 2, 2007. Coordinate data are available in PDB, mmCIF, and XML formats. The date and time stamp of each file indicates the last time the file was modified.

Scripts are available to automatically download data:

Entries in the PDB archive have been processed by the three members of the wwPDB (RCSB PDB, MSD-EBI, and PDBj).

back to top

16-January-2007

PDB File Formats, Annotation Procedures, and Remediation

wwPDB members work to annotate all data deposited to the PDB archive. Information about data file formats, annotation procedures, and remediation efforts are described below.

  • File Format Guides

    Documentation for the different file formats for PDB data is available at http://www.wwpdb.org/docs.html

    Entries in PDB format comply with the PDB Contents Guide v2.3 (July 1998).
    Entries in mmCIF format comply with the PDB Exchange Dictionary v1.037 (January 2007).
    Entries in XML format comply with the PDBML Schema v1.037 (January 2007).

  • Annotation Procedures

    Annotation procedures and policies are described at http://www.wwpdb.org/docs.html

    There are some data items for which the processing procedures are ambiguous. Over the course of the last 12 months, the annotation teams have worked to formalize many aspects of PDB annotation policies and procedures. As a result, a consistent set of annotation procedures are being defined.

  • Remediation

    Remediation project information is available at http://remediation.wwpdb.org/.

    All existing entries have been reviewed and errors have been corrected where possible. One major change is that the atomic names will conform to IUPAC standards. In addition, the chemical component dictionary has been updated and extended to include more information about the chemical structures of each component. The wwPDB Advisory Committee has reviewed and approved this effort.

    Please consult this site to review test data files and the new dictionary. The full new data set in PDB, mmCIF and XML formats will become available for review in April 2007.

  • Questions about these projects should be sent to info@wwpdb.org.

    09-January-2007

    Browsing the PDB Using Medical Subject Headings (MeSH)

    The RCSB PDB's " Browse Database" resources allow users to explore the PDB archive using different hierarchical trees. The Medical Subject Headings (MeSH) Browser searches the PDB using an index of biomedical-related publications from the National Library of Medicine ( NLM).

    The primary citations for structures in the PDB are used to retrieve the MeSH terms associated with their respective PubMed IDs. This mapping of the PDB IDs and the MeSH terms is then loaded into the database. The MeSH tree is constructed using the hierarchy obtained from the MeSH site.

    Nodes of the tree are populated with structures whose primary citations are associated with the MeSH term for each node. Clicking on the folder icon beside each node further opens up the sub folders for that node. Selecting the term itself will retrieve all associated structures. The text box available at the top of the page can be used to search the tree using MeSH index number.

    For example, several more folders are revealed when the folder for the MeSH leaf node 'CO2: Virus Diseases' is opened. The folder for Tumor Virus Infections can then be opened to find all structures indexed as relating to Epstein-Barr Virus Infections (MeSH Number C02.929.313).

    Top folder 'C11: Eye Diseases' can be opened to find structures indexed as relating to eye diseases, specifically cataracts (MeSH Number C11.510.245).

    Other browsers can be used to navigate structures based upon hierarchical trees relating to biological process, cellular component, molecular function, enzyme classification, source organism, genome location, SCOP, and CATH. These browsers are available from the " Search" tab in the left-hand menu on the RCSB PDB home page.

    02-January-2007

    PDB Focus: Weekly Deadlines for Release/Modify Entry Requests

    PDB entries are processed by three members of the wwPDB ( RCSB PDB, MSD-EBI, and PDBj) and are released immediately (REL), when the corresponding paper is published (HPUB), or on a particular date (HOLD).

    Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release.

    When the release of HPUB structures is requested, the wwPDB routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update.

    To be included in the next weekly update, any required author correspondence should be sent to the appropriate wwPDB member by the following times:

    All entries due for release are transferred to the RCSB PDB for final packaging into the master PDB ftp archive. These files are then released by 4:00 EST each Wednesday.

    Requests received after these cutoff times will be processed during the next update cycle.