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Year 2005 News

Contents:

20-Dec-2005 Happy Holidays from the RCSB PDB
13-Dec-2005 PDB Focus: Ligand Depot--a Small Molecule Information Resource
06-Dec-2005 RCSB PDB Focus: Help system for beta site, depositing structures, and more
29-Nov-2005 PDB Focus: Restarting ADIT depositions
22-Nov-2005 Workshop for High School Teachers and Students: Building Protein Models at the Science Olympiad
15-Nov-2005 RCSB PDB's 2005 Annual Report Now Available
08-Nov-2005 Online Tutorial Guides Users Through New Beta Site
01-Nov-2005 Fall Newsletter Published
25-Oct-2005 RCSB Beta Site Focus: Searching and Browsing for Structures in the PDB
18-Oct-2005 New Beta Site Will Replace the Current RCSB PDB Portal on January 1, 2006
11-Oct-2005 PDB Focus: First Time Depositors...
04-Oct-2005 RCSB PDB Exhibit, Workshop for New Jersey Science Teachers
04-Oct-2005 Looking at the Functional Distribution of Structural Genomics: Related Tool Online and Paper Published
27-Sep-2005 PDB Focus: Beta FTP Site Organized by Experimental Type
20-Sep-2005 New Structural Genomics Portal Available
13-Sept-2005 RCSB PDB Poster Prize Awarded at IUCr Meeting
06-Sept-2005 mmCIF articles published in new edition of the International Tables for Crystallography (Volume G)
30-Aug-2005 Molecule of the Month Features Available as Individual PDFs
23-Aug-2005 PDB Focus: Beta FTP Site Organized by Experimental Type
16-Aug-2005 RCSB PDB at IUCr: wwPDB Booth, Presentations, and More
09-Aug-2005 Summer Newsletter Published: Protein Modeling for High School Students, PDBML/XML Files, and More...
02-Aug-2005 PDB Focus: Releasing HOLD and HPUB structures
26-Jul-2005 Announcing a beta FTP site organized by experimental type
19-Jul-2005 PDB Focus: Tips for depositing multiple related structures using ADIT
12-Jul-2005 Data Distribution on DVD
05-Jul-2005 Second Phase of Protein Structure Initiative (PSI)
28-Jun-2005 RCSB Poster Prize awarded at ACA
21-Jun-2005 RCSB Poster Prize awarded at RECOMB
21-Jun-2005 ISMB Meeting: Exhibit Booth and Education Session Presentation
14-Jun-2005 PDBML/XML data uniformity files
07-Jun-2005 Beta Site Focus: Molecular Viewers
31-May-2005 PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site
24-May-2005 Come visit us in "Data Alley" -- RCSB PDB Demonstrations, Poster Prize, Workshops, and More at the ACA Annual Meeting May 28 - June 2, 2005 in Orlando, FL
17-May-2005 RCSB PDB Exhibit and Art Show at ACS Mid-Atlantic Regional Meeting
17-May-2005 RCSB PDB Educational Resources Poster
10-May-2005 Spring Newsletter Published: Beta Site Features, Community Focus on Stephen K. Burley, Education Corner by Judith Voet, and More
03-May-2005 Beta Site Focus: "SearchFields" Advanced Search Interface
26-Apr-2005 PDB Focus: pdb_extract Makes Deposition Easier
19-Apr-2005 Education Focus: DNA Day
19-Apr-2005 Art of Science Exhibit opens at Texas A&M University
12-Apr-2005 RCSB PDB Focus: Help desks for beta site feedback, deposition information, and more
05-Apr-2005 Our best wishes to Gary
05-Apr-2005 Beta Site Focus: Improved Searching and Visualization for Ligands
29-Mar-2005 RCSB PDB Education Activities: ASBMB and NSTA
22-Mar-2005 Status Report on "Large Macromolecular Complexes in the Protein Data Bank" Published
15-Mar-2005 ASBMB Meeting: RCSB Exhibit Booth and Education Symposium
08-Mar-2005 Physical Model of February's Molecule of the Month - Major Histocompatibility Complex - Available on Loan to Educators
01-Mar-2005 Beta Site Focus: Query-by-Example in Structure Explorer Pages
01-Mar-2005 Structural Genomics Focus: NIGMS Project Yields More Than 1,000 Protein Structures
22-Feb-2005 Time-stamped Copies of PDB Archive Available via FTP
22-Feb-2005 Art and Science Events Unfurl...
15-Feb-2005 PDB Focus: Weekly Deadlines for Release/modify entry requests
08-Feb-2005 RCSB PDB Exhibit at the Biophysical Society Meeting
01-Feb-2005 Beta Site Focus: New Customizable Tabular and Structure Reports
25-Jan-2005 Winter Newsletter Published: A Look at 2004 Depositions, Early Protein Structures, Beta Site Features, and More
18-Jan-2005 PDB Focus: Changes and Corrections to Entries in the PDB Archive
11-Jan-2005 2004 Deposition Statistics
04-Jan-2005 PDB Data Distributed on CD-ROM and DVD in 2005
04-Jan-2005 RCSB Beta Site Focus: Detailed Help System

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


20-Dec-2005

Happy Holidays from the RCSB PDB

Happy Holidays

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

13-Dec-2005

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

Ligand Depot 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@deposit.rcsb.org.

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.

06-December-2005

RCSB PDB Focus: Help system for beta site, depositing structures, and more

Electronic help desks and an integrated help system are available to support users navigating the RCSB PDB.

betafeedback@rcsb.org responds to emailed bugs and comments about pdbbeta.rcsb.org. The beta site help system launches into a separate browser window to allow users to access the help information and the beta site at the same time. It offers detailed topics (including Getting Started, Download Files, Search/Browse the Database, and Results), an index, glossary, and a search engine.

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. Questions about searching, reporting, and using all of the resources available from the RCSB PDB should be sent to this address.

29-November-2005

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.

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.

22-November-2005

Students building protein models
Protein modeling at the Wisconsin Science Olympiad, as described by Gary Graper an the RCSB PDB Newsletter's Education Corner.

Workshop for High School Teachers and Students: Building Protein Models at the Science Olympiad

"Protein modeling" -- where students build physical 3D models of proteins -- will be a trial event at the Northern Regional and State Final 2006 Science Olympiads in NJ.

This event will challenge high school students to explore structure and the relationship of structure to protein function using computer visualization and physical modeling tools. Students are introduced to the resources of the RCSB PDB, learn how to use RasMol, and create protein structures using 'Mini-Toobers' from 3D Molecular Designs.

The RCSB PDB team will be judging the models at the olympiad and providing the materials for the event.

A training workshop will be held at the RCSB PDB at Rutgers, The State University in Piscataway, NJ on Wednesday, December 7, 2005. Tim Herman (MSOE Center for BioMolecular Modeling) will be onhand to demonstrate how the Mini-Toobers can be used to generate a protein model.

Further details about this workshop and event are available at http://education.pdb.org/olympiad/.


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15-November-2005

PDB 2005 Annual Report

RCSB PDB's 2005 Annual Report Now Available

The RCSB Protein Data Bank's Annual Report, which covers the period of July 1, 2004 - June 30, 2005, is currently being distributed.

This 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 describes the many different activities in data deposition, data access, and education and looks at the features of the new beta site.

If you would like a printed copy of the report, please send mail to info@rcsb.org.


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08-November-2005

New Beta Site Screenshot

Online Tutorial Guides Users Through New Beta Site

A narrated demonstration is available to help users explore the new features of the beta website. This short tutorial provides an excellent overview for searching, navigating, generating reports, visualizing structures, and browsing PDB data.

The new beta site will replace the current RCSB PDB portal on January 1, 2006.


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01-November-2005

Fall Newsletter Published

New Beta Site and Interviews with William L. Duax (International Union of Crystallography and Hauptman-Woodward Medical Research Institute) and Miriam Rossi (Vassar College)

The Fall 2005 issue of the RCSB PDB Newsletter has been published in HTML and PDF formats. Highlights include a look at the new beta site that will become 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.

The printed version of the newsletter has been redesigned to make it easier to read and to find articles of interest. 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 .

25-October-2005

RCSB Beta Site Focus: Searching and Browsing for Structures in the PDB

The Search Tab on the new RCSB PDB beta site offers many different ways of accessing the structures contained in the PDB archives. Forms are available for searching the PDB archives by PDB ID, Swiss-Prot ID, ligand, and sequence. A separate form can be used to search for theoretical models.

The Latest Release option displays images and summary information for the structures added to the archives in the most recent update. Unreleased structures can be searched by ID, title, authors, and possibly sequence.

The Queries tab shows all searches performed during the current web session. The results of these searches can also be retreived.

Several simple text-based search options are also available on every page of the new site. Users can search the PDB archives using specific PDB IDs, keywords, or authors; run text searches on the static webpages; or search the archives and static webpages at the same time.

Browsers are available to navigate structures using classifications from Gene Ontology, EC nomenclature, source organism, disease, genome, SCOP, and CATH. Users can explore each category's hierarchy, view the number of associated PDB structures, and search for specific related structures. For example, the Disease Browser can be used to look at diseases involving the nervous system, such as fragile X syndrome and Tay-Sachs Disease. Selecting a disease of interest (e.g., Alzheimer Disease) will return all of the structures associated with that disease.

For all searches, the resulting list of structures can be sorted, downloaded, used to create a tabular report (e.g., citation or sequence information), or further refined by combining the search with another query.

This new site will replace the current RCSB PDB portal on January 1, 2006.

Additional comments should be sent to betafeedback@rcsb.org.


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18-October-2005

New Beta Site Will Replace the Current RCSB PDB Portal on January 1, 2006

To provide a powerful portal for studying the structures of biological macromolecules and their relationships to sequence, function, and disease, the RCSB has enhanced and revised the RCSB web and FTP sites.

We encourage you to test and review http://pdbbeta.rcsb.org and ftp://ftpbeta.rcsb.org before these resources replace the versions currently in production at www.pdb.org and ftp.rcsb.org on January 1, 2006.

The enhanced web design offers improved navigation for easily locating the resources and tools offered by the RCSB PDB. An always-present left hand menu makes features and resources related to structural genomics, education, and software easily attainable.

The search tab offers different ways of accessing the RCSB PDB database, including a new method for "browsing" through structures grouped in categories related to disease, molecular function, biochemical process, or cellular location.

The reengineered database is based upon the PDB data that has been remediated and standardized. Tools to examine these data include: improved ligand searching; a clear distinction between the reported primary and derived data; and the integration of external data resources currently not available on the production site.

A searchable help system with a glossary and user guide provides detailed information for accessing the website, database, and for understanding PDB data. A narrated presentation in Flash is linked from the beta site homepage to guide users through searching, navigating, generating reports, visualizing structures, and browsing PDB data.

Thanks to everyone who has contributed to the development of this resource through their feedback. Additional comments should be sent to betafeedback@rcsb.org.


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11-October-2005

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 is accurate and reflects 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.
  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"


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04-October-2005

RCSB PDB Exhibit, Workshop for New Jersey Science Teachers

An RCSB exhibit booth and workshop presentation will be part of the New Jersey Science Conference (October 5-6 in Somerset, NJ). The conference is co-sponsored by the New Jersey Science Teachers Association and the New Jersey Science Education Leadership Association. Shuchismita Dutta will present "Seeing is believing but meeting is better" to introduce the educational resources of the RCSB PDB to science teachers. Gary Graper (Event Supervisor, Wisconsin Science Olymipad) and Jennifer Morris (Center for BioMolecular Modeling) will give a hands-on demonstration to show how protein modeling can be a successful event at the NJ Science Olympiad.


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04-October-2005

Looking at the Functional Distribution of Structural Genomics: Related Tool Online and Paper Published

The RCSB PDB's structural genomics portal provides a tool that can be used to explore the distributions of functions found among structural genomics structures, PDB structures, genomes, and homology models. This functional coverage can be examined according to Enzyme Classification, Gene Ontology (biological process, cell component, or molecular function), and Disease.

A paper describing the methodology of this tool has been published: Lei Xie and Philip E. Bourne (2005) Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models. PLoS Comput Biol 1(3): e31


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27-September-2005

PDB Focus: Beta FTP Site Organized by Experimental Type

The RCSB has introduced a new ftp site designed to address the increasing number and diversity of structure entries. Entries within ftp://ftpbeta.rcsb.org are organized by the method of structure determination. This new ftp structure distinguishes entries obtained from X-ray and neutron diffraction, NMR, electron microscopy, or theoretical modeling techniques.

Within each structure determination category are directories containing files for entries in mmCIF, PDB, and XML formats; biological unit files; and the structure factor or restraint files. Individual entries are stored in a collection of 2-letter code subdirectories corresponding to the middle characters of the 4-letter PDB identifier.

All entries in the new ftp site are compressed using the GNU gzip utility. For example, the PDB format file for entry 4HHB is found at ftp://ftpbeta.rcsb.org/pub/data_by_method/x-ray_neutron_methods/entries/pdb/hh/pdb4hhb.ent.gz.

This beta ftp site is updated weekly in conjunction with the current ftp site, ftp://ftp.rcsb.org. Both ftp sites will be maintained through December 2005. After this time, only the new organization will be supported.

For comments about the beta FTP send mail to betaftp@rcsb.rutgers.edu.


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20-September-2005

Structural Genomics Portal ScreenShot

New Structural Genomics Portal Available

The RCSB PDB offers online tools, summary reports, and target information related to structural genomics from a new information portal at sg.pdb.org.

Information and links are provided for the structural genomics initiatives located worldwide, including reports for each center that provide target lists, target status progress, targets in the PDB, and sequence redundancy analyses.

Databases that track the progress of protein studies are available. TargetDB contains information about the progress of the production and solution of structures. PepcDB extends the content of TargetDB with status history, stop conditions, reusable text protocols and contact information collected from the PSI Centers.

A tool is also provided to explore the distributions of functions found among structural genomics structures, PDB structures, genomes, and homology models. This functional coverage can be examined according to Enzyme Classification, Gene Ontology (Biological Process, Cell Component, or Molecular Function) and Disease.


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13-September-2005

IUCR Poster Prize Winner

RCSB PDB Poster Prize Awarded at IUCr Meeting

Thanks to the students and judges who participated in the RCSB PDB Poster Prize at this year's XX Congress & General Assembly of the International Union of Crystallography (IUCr August 23 - 31 in Florence, Italy).

The award went to "Proline isomerisation in stefin B: A crucial step towards amyloid fibril formation" by Sasa Jenko Kokalj, Gregor Guncar, Eva Zerovnik, and Dusan Turk (Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia).

Special thanks to the judging committee -- Maria-Armenia Carrondo (Chair), Carlos Frazao, Ramakumar Suryanarayanarao, Xiao-Dong Su, Edward Mitchell, Marius Jaskolski.


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06-September-2005

mmCIF articles published in new edition of the International Tables for Crystallography (Volume G)

Several articles describing the macromolecular Crystallographic Information File format (mmCIF) and how it is used at the RCSB PDB are in the recently-published International Tables for Crystallography Volume G: Definition and Exchange of Crystallographic Data.

Included in this reference guide for programers, data managers, and crystallographers are in-depth articles that will aid in the design of interoperable computer applications, including "Classification and use of macromolecular data", "Macromolecular dictionary (mmCIF)", "Specification of the Crystallographic Information File", "The Protein Data Bank exchange data dictionary", "The use of mmCIF architechture for PDB data management", and "Specification of a relational Dictionary Definition Language (DDL2)".

This volume was edited by S.R. Hall, and B. McMahon, and published for the International Union of Crystallography by Springer (Dordrecht, The Netherlands) in 2005. Order information is available at http://journals.iucr.org/iucr-top/it/itg/itg.html.


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30-August-2005

Molecule of the Month Features Available as Individual PDFs

The Molecule of the Month (MOM) series presents short accounts that describe selected molecules from the PDB. These online chapters are now available as downloadable PDFs and can be easily shared, printed, or incorporated into classroom lessons. Users can download individual MOM features by going to the Molecule of the Month Alphabetical Listing and clicking on the PDF link displayed after the molecule title.

Each installment includes an introduction to the structure and function of the molecule and relates the molecule to human health and welfare. Suggestions for viewing structures on the RCSB PDB website and for additional reading are also provided. Produced and illustrated by David S. Goodsell since 2000, the Molecule of the Month is a proven resource for the classroom. Previous MOM features have explored structures such as actin, collagen, DNA, green fluorescent protein, ribosome, and transfer RNA.


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23-August-2005

PDB Focus: Beta FTP Site Organized by Experimental Type

The RCSB has introduced a new ftp site designed to address the increasing number and diversity of structure entries. Entries within ftp://ftpbeta.rcsb.org are organized by the method of structure determination. This new ftp structure distinguishes entries obtained from X-ray and neutron diffraction, NMR, electron microscopy, or theoretical modeling techniques.

Within each structure determination category are directories containing files for entries in mmCIF, PDB, and XML formats ; biological unit files ; and the structure factor or restraint files. Individual entries are stored in a collection of 2-letter code subdirectories corresponding to the middle characters of the 4-letter PDB identifier.

All entries in the new ftp site are compressed using the GNU gzip utility. For example, the PDB format file for entry 4HHB is found at ftp://ftpbeta.rcsb.org/pub/data_by_method/x-ray_neutron_methods/entries/pdb/hh/pdb4hhb.ent.gz.

This beta ftp site is updated weekly in conjunction with the current ftp site, ftp://ftp.rcsb.org. Both ftp sites will be maintained through December 2005. After this time, only the new organization will be supported.

Questions or comments about the beta FTP site should be sent to betaftp@rcsb.rutgers.edu.


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16-August-2005

wwPDB logo

RCSB PDB at IUCr: wwPDB Booth, Presentations, and More

The beta RCSB PDB website, along with tools for deposition, will be demonstrated at the wwPDB exhibit stand (Booth number 12) at this year's XX Congress & General Assembly of the International Union of Crystallography (IUCr August 23 - 31 in Florence, Italy). Our wwPDB partners MSD-EBI and PDBj will also demonstrate their websites and we will all be available throughout the exhibition to meet with PDB users. Other activities include:

  • Kyle Burkhardt will present Deposition and Validation using RCSB PDB Tools as part of the CCP4 Workshop on Tuesday, August 23 in Cimabue Hall.

  • A Round Table on Data Mining from the PDB will be held on August 27 in the Cimabue Hall at 12:35 p.m., with presentations from Helen M. Berman, Kim Henrick, Haruki Nakamura, and Philip E. Bourne.

  • The RCSB PDB Poster Prize will be awarded to the best student poster at the meeting. The award will be selected by a committee chaired by Maria Arm´┐Żnia Carrondo (Universidade Nova de Lisboa) and announced at the awards ceremony.

  • Helen Berman will describe How the RCSB validates PDB Structures. during the microsymposia Improving Structures Using Bioinformatics (August 26, 10:00 - 12.35 p.m. in the Leonardo da Vinci room).

  • Zukang Feng will discuss mmCIF Applications at the RCSB Protein Data Bank during the COMCIFS Open Commission Meeting on the Current Status and Future Prospects of CIF (August 26, 12:35 - 14.35 p.m. in the Leonardo da Vinci room).


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09-August-2005

Summer Newsletter

Summer Newsletter Published: Protein Modeling for High School Students, PDBML/XML Files, and More...

The Summer 2005 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. Highlights include a Community Focus discussion with Robert Sweet (Brookhaven National Laboratory), and an Education Corner feature that describes the Protein Modeling event held at the Wisconsin Science Olympiad for high school students. This issue also highlights the files from the data uniformity project released in PDBML/XML format.

The printed version of the newsletter has been redesigned to make it easier to read and to find articles of interest. 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.


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02-August-2005

PDB Focus: Releasing HOLD and HPUB structures

Structure data can be held for a maximum period of one year between the deposition and release of any entry, regardless of the deposited status.

Data can be always be released before the paper is published. The citation information can be updated at a later date.

When a structure has been on hold for a year, we ask the author to release or withdraw the structure. Withdrawn entries can be redeposited at a later time.

We try to release HPUB files as close to the publication date as possible. The PDB receives publication dates and citation information from some journals. For other journals, the PDB scans the literature for publication information (using the deposited author names and deposited article title). We also greatly appreciate the citation information that is sent to us at deposit@deposit.rcsb.org from the community.

26-July-2005

Announcing a beta FTP site organized by experimental type

The RCSB is introducing a new ftp site design to address the increasing number and diversity of structure entries. Entries within ftp://ftpbeta.rcsb.org are organized by the method of structure determination. This new ftp structure distinguishes entries obtained from X-ray and neutron diffraction, NMR, electron microscopy, or theoretical modeling techniques.

Within each structure determination category are directories containing files for entries in mmCIF, PDB, and XML formats; biological unit files; and the structure factor or restraint files. Individual entries are stored in a collection of 2-letter code subdirectories corresponding to the middle characters of the 4-letter PDB identifier.

All entries in the new ftp site are compressed using the GNU gzip utility. For example, the PDB format file for entry 4HHB is found at ftp://ftpbeta.rcsb.org/pub/data_by_method/x-ray_neutron_methods/entries/pdb/hh/pdb4hhb.ent.gz.

This beta ftp site is updated weekly in conjunction with the current ftp site, ftp://ftp.rcsb.org. Both ftp sites will be maintained through December 2005. After this time, only the new organization will be supported.

Questions or comments about the beta FTP site should be sent to betaftp@rcsb.rutgers.edu.

19-July-2005

PDB Focus: Tips for depositing multiple related structures using ADIT

When depositing many structures that are related to one another, there are a few ways of making the ADIT process simpler:

  • Structures solved using X-ray crystallography should be prepared using pdb_extract before using ADIT. This will minimize manual typing and save time during deposition. pdb_extract takes information about data collection, phasing, density modification, and the final structure refinement from the output files and log files produced by the various applications used for structure determination. The collected information is organized into a file ready for deposition using ADIT. Information duplicated in all entries (author name, citation information, protein names, etc.) can be included in a text file that is prepared once and used for running pdb_extract for each entry. After pdb_extract has combined all the available information into a single file for each structure, ADIT can be used for quick deposition.
  • A similar tool is being developed for structures solved by other experimental methods. For these structures, deposit one representative structure following the instructions provided at deposit.pdb.org. Then write to deposit@deposit.rcsb.org to let us know about the other related entries. Once the first entry has been annotated, processed and finalized, it can be used as a template for your subsequent depositions. For each structure, replace the coordinates and update the information in the header section of the PDB file as necessary to prepare the related files for deposition.
  • If the structures have ligands, drugs or inhibitors bound to them, please check Ligand Depot and match the 3 letter code in the file to the one used in the chemical component dictionary. If the ligand is not present in the dictionary, please email detailed information (complete chemical name, 2D figure showing connectivity, bond order and sterochemistry) along with the RCSB and PDB IDs of the entries they are associated to expedite the processing of these files.

12-July-2005

Data Distribution on DVD

As of 2005, the PDB archives will be made available as an annual DVD product. The CD-ROM product has been discontinued.

The PDB has historically distributed coordinate data through the mail; starting in 1990, the data were produced on CD-ROM. In addition to the rapid increase in the number and size of structures of the archives, the number of formats to distribute has also increased (now PDB, mmCIF, and PDBML/XML). Currently, it would take over 50 disks to distribute the archives on CD-ROM.

To minimize the difficulty of producing (and keeping up with a large number of CDs), the RCSB PDB began distributing an incremental set of data each quarter, starting with April 2003. Instead of four full copies of the archive, subscribers would receive a copy of the full archive at the beginning of the year, followed by three quarterly sets of data that would include structures released and/or modified during the three-month period.

Starting in January 2005, ftp://snapshots.rcsb.org/ was created to hold time-stamped yearly snapshots of the PDB Archives. This was done as part of a wwPDB initiative (wwpdb.org). The first snapshot directory contains the exact and complete contents of the FTP archive as it appeared on January 6, 2005. These data, along with data in XML/PDBML format, were also made available as an 8 DVD release. A similar release on CD-ROM would require 50 disks.

The wwPDB will produce one DVD set per year of the entire PDB archive in PDB, mmCIF, and XML/PDBML format.

For new orders, please email your postal address to cddvd@rcsb.rutgers.edu. New orders will be filled in the order that they are received until supplies are exhausted. Please allow several weeks for delivery.

05-July-2005

Second Phase of Protein Structure Initiative

The NIH has announced the awards for the second phase of the Protein Structure Initiative (PSI). The details of the awards are described at http://www.nigms.nih.gov/news/releases/070105.html.

Additional information about the NIH PSI program can be obtained at http://www.nigms.nih.gov/psi/.

28-June-2005

Poster Prize Winner M. Adams
ACA poster prize winner M. Adams

RCSB Poster Prize awarded at ACA

Thanks to the students and judges who participated in the RCSB PDB Poster Prize at the American Crystallographic Association's Annual Meeting (May 28-June 2, 2005; Orlando, FL).

The award went to "Safety in Cycling: Novel Redox Proteins from Escherichia coli" by Melanie A. Adams and Zongchao Jia (Queen's University).

Special thanks to the judges -- Craig Ogata, Michael Sawaya, Marilyn Yoder, and Jim Pflugrath (chair) -- and to David Rodgers for organizing.

21-June-2005

RCSB Poster Prize awarded at RECOMB

Thanks to the students and judges who participated in the RECOMB & PDB Poster Awards recognizing insight and innovation in structural computational biology at the Ninth Annual International Conference on Research in Computational Molecular Biology (May 14-18, Cambridge, MA).

Awards went to:

Comparative Modeling of Mainly-Beta Proteins by Profile Wrapping
Andrew V. McDonnell, Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen, Bonnie Berger, MIT

MAPPIS: Multiple Alignment of Protein-Protein Interfaces
Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov and Haim J. Wolfson, Tel-Aviv University

The judging committee (organized by Simon Kasif and Gus Cervini) was comprised of Bonnie Berger (MIT), Peter Clote (BC), Enoch Huang (Pfizer Discovery), Simon Kasif (Boston University), Jun Liu (Harvard), T.M. Murali (VPI), Fritz Roth (Harvard Medical School), Russell Schwartz (CMU), Lei Shen (Harvard), and Mona Singh (Princeton).

21-June-2005

ISMB Meeting: Exhibit Booth and Education Session Presentation

The RCSB PDB will be part of the 13th Annual Meeting of the International Society for Computational Biology being held June 25 - 29 in Detroit, Michigan.

Demonstrations of the RCSB PDB beta site will be given at the exhibit booth (#15).
Wolfgang Bluhm will be presenting "Structural Bioinformatics Education from the RCSB Protein Data Bank" as part of International Society for Computational Biology (ISCB) Education session on Sunday, June 26.
We hope to see you there.

14-June-2005

PDBML/XML data uniformity files

After an extended period of beta testing, the remediated PDB data files from the data uniformity project are now available in PDBML/XML format on the production FTP archive in the following directories:

The files in the XML directory contain separate XML tags for each item in the atom-site category. XML-extatom files contain the atom records only, in an alternate format with only one pair of XML tags for each atom. XML-noatoms files contain only the metadata for each structure and no atom records. All files are gzipped (.gz compressed). In each case, the data files are in the usual hash directories according to the middle two characters of the PDB ID (e.g. the files for 100d are in a hash directory 00).

Comments are welcome at info@rcsb.org.

07-June-2005

KiNG, Jmol, and WebMol viewers
KiNG, Jmol, and WebMol viewers
(click on image for side by side comparison)

Beta Site Focus: Molecular Viewers

The RCSB PDB's beta Web site features three third-party molecular viewers for interactively visualizing structures:

  • KiNG (Kinemage, Next Generation), written by Ian Davis (KiNG home page)
  • Jmol, an open source molecule viewer (Jmol home page)
  • WebMol, written by Dirk Walther (WebMol home page)

On each Structure Explorer page (e.g. for 1J59), links to all three viewers are found in the "Viewers" section (underneath the still image of the molecule). All three viewers require a Java enabled browser but not any additional plug-ins or helper installations. However, some applets may require the user to accept a security certificate upon first download (click "Yes" or "Always").

All three viewers offer rich functionality for visualizing molecules, with many options for selecting, rendering, and coloring portions of or entire PDB structures.

KiNG, by default, presents a colored ribbon diagram of the structure. The top menu contains many visualization options, along with additional tools, and the ability to save and later reload the currently displayed view. The right hand panel contains a list a check boxes that determine which molecular entities in the structure file are being displayed. This option extends to the models in NMR structures, and is therefore particularly convenient for comparing multiple NMR models in a single PDB file.

Jmol offers a large number of options for selecting portions of a structures and rendering them in different ways (for example showing a space filled representation of a ligand and a ribbon diagram of the main protein chain). This can be accomplished by right clicking on the applet, and by choosing from the cascading menu the appropriate options for "Select", "Render", and "Color". Other convenient features include the ability to continuously spin the structure, or to visualize the crystal axes or unit cell boundaries.

WebMol presents a stick model of the molecule with several options for coloring (e.g. by chain or by B-factor). Dotted molecule surfaces can also be displayed. Distance matrix plots or Ramachandran plots can be opened in a separate window, which is interactively linked to the display of the molecule.

For further help, information about these viewers is provided --KiNG and WebMol help are available from within the applets, Jmol help is available at the Jmol home page).

Comments about the RCSB PDB beta Web site in general, and about the use of the viewers on the beta Web site in particular, are welcome at betafeedback@rcsb.org.

31-May-2005

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

The results of the weekly clustering of protein chains in the PDB are posted at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/. These clusters are used in the "remove similar sequences" feature on SearchLite and SearchFields on the PDB web sites.

Files that list the clusters and their rankings at 50%, 70% and 90% sequence identity are available. Smaller rank numbers indicate higher (better) ranking. Chains with rank number 1 are ranked as the best representative of their cluster.

The contents of these files and the details of the clustering and ranking are further described at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/README and http://www.rcsb.org/pdb/redundancy.html.

24-May-2005

RCSB PDB at ACA 2004
The RCSB PDB Exhibit booth at the 2004 ACA meeting
(click on image for full size picture)

Come visit us in "Data Alley" -- RCSB PDB Demonstrations, Poster Prize, Workshops, and More at the ACA Annual Meeting May 28 - June 2, 2005 in Orlando, FL

The RCSB PDB will be actively participating in the Annual National Meeting of the American Crystallographic Association (ACA). 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 also be featured.

Workshops. Annotator Kyle Burkhardt will be presenting a tutorial on using deposition and validation software at the "A Protein Crystallographic Toolbox: CCP4 Software Suite" workshop being held on Saturday, May 28.

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 educational books. An announcement will appear on the website and newsletter. The RCSB PDB Poster Prize will also be awarded at the XX Congress of the International Union of Crystallography (IUCr).

17-May-2005

MARM meeting

RCSB PDB Exhibit and Art Show at ACS Mid-Atlantic Regional Meeting

At the American Chemical Society's MARM Meeting at Rutgers University (Piscataway, NJ), the RCSB PDB will be part of the exhibition. Images from the RCSB PDB's Art of Science show will also be on display at The Gallery, a space dedicated to art exhibits at Rutgers University where the meeting will be taking place. MARM will be at Rutgers May 22 - 25, 2005.

We hope to see you there!

17-May-2005

Education Poster
Education Poster
(click on image for full-sized poster)

RCSB PDB Educational Resources Poster

Resources for education available from the RCSB PDB are highlighted on a poster that is available for download (PDF; 8 1/2 by 11 inches) and will be on view at conferences over the summer.

  • The Molecule of the Month features illustrate important biological molecules and how they function through descriptive text, pictures, and links to specific PDB entries and other resources.
  • The RCSB PDB Newsletter regularly features interviews with members of the community and descriptions of how the PDB is used in all levels of education.
  • The Education Page provides resources for learning about Proteins and Nucleic Acids, answering the question "What is the PDB?", protein documentaries, and suggested reading materials and links.
  • A number of tools for finding and visualizing proteins are available for use in the classroom, including molecular images available for download, links to information found in journals, and keyword queries that can locate specific proteins.

10-May-2005

Spring Newsletter Published: Beta Site Features, Community Focus on Stephen K. Burley, Education Corner by Judith Voet, and More

The Spring 2005 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. Highlights include a Community Focus look at Stephen K. Burley (Structural GenomiX, Inc.) and an Education Corner by Judith Voet (Swarthmore College). This issue highlights beta site features, time-stamped copies of the PDB archive, and information about making changes, corrections, and releasing PDB entries.

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 here.

03-May-2005

SearchFields Advanced Search Interface
SearchFields Advanced Search Interface
(click on image for full-sized screen shot)

 

Beta Site Focus: "SearchFields" Advanced Search Interface

The advanced search interface of the RCSB PDB's beta Web site can be accessed by clicking on Search Database and then SearchFields in the yellow navigation bar on the left side of the Web page. This search interface allows users to construct powerful queries using a large number of specific data fields.

The starting point for a query is the black and white menu bar with the menu items Summary, Materials & Methods, Structure Details, Biology & Chemistry, and Reference. Moving the mouse over any of these items reveals a list of submenus, such as Summary > Title/Text and Summary > Deposition/Release Date. Clicking on one of these submenu items then brings up a page in which individual search fields can be filled in with the desired query terms.

When multiple search fields are filled in, the query must satisfy all submitted query terms (i.e. an "AND" query is performed). Items can be picked from different menu and submenu items. For example, to search for all NMR structures which were published in Nature and for which experimental data (i.e. NMR restraints) are available, proceed as follows:

  • Select Materials & Methods > Experiment Type/Data Availability
  • Click the Yes button to the right of Exp. Data Available
  • Select NMR from the pull down menu to the right of Exp. Technique
  • Select Reference > Citation
  • Type Nature into the search box to the right of Journal Name
  • In the gray bar on top, a button called New Search should be selected
  • Press Submit Query

At the time of this writing, the above query returned 52 results. To further refine this search, select Query > Query Refinement > Refine Using Search Form. This returns you to the SearchFields page. Notice, however, that the Refinement button is now selected in the gray bar. Select AND, OR, or BUTNOT from the pull down menu next to Refinement, fill in any desired query terms as before, and press Submit Query. This would now further refine the previous query according to the chosen logic.

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

26-Apr-2005

PDB extract

PDB Focus: pdb_extract Makes Deposition Easier

pdb_extract helps depositors automatically prepare crystal structure depositions. This software tool extracts information about data collection, phasing, density modification, and the final structure refinement from the output files output files produced by many applications used for structure determination. The collected information is organized into an mmCIF file that is ready for deposition. Since pdb_extract fills in many data fields in this mmCIF file, fewer data items have to be manually entered -- saving time and minimizing errors.

The online version of pdb-extract is used to upload output files and create mmCIF files. The files can be used as input to ADIT for a complete deposition.

pdb_extract can be downloaded in source and binary versions for Linux, SGI, SUN, OSF and Mac OSX from http://sw-tools.pdb.org/. Source and Linux binary versions of ADIT are also available.

pdb_extract is also part of the CCP4i interface.

Questions and comments may be sent to deposit@deposit.rcsb.org.

19-Apr-2005

DNA Day 2005

Education Focus: DNA Day

Monday April 25 will be the third "National DNA Day". 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:

  • The National Human Genome Research Institute will be sponsoring an online webcast and chatroom on DNA Day, in addition to providing a variety of teaching materials (http://www.genome.gov/DNAday/).
  • The Nucleic Acid Database is a repository of three-dimensional structural information about nucleic acids. The NDB has a searchable database and a browsable Atlas that provides summary information and images for each structure in the database (http://ndbserver.rutgers.edu/).
  • The PDB has many education resources related to nucleic acid structure, including DNA's turn as Molecule of the Month in November 2001.
  • The Nature Publishing Group has compiled the original articles, historical perspectives, and examinations of DNA in medicine, society, and as a biological molecule in "Double Helix: 50 years of DNA" (http://www.nature.com/nature/dna50/).

19-Apr-2005

Art Of Science Exhibit
The exhibit at Farleigh-Dickinson University

Art of Science Exhibit opens at Texas A&M University

Images from the RCSB PDB's "Art of Science" exhibit are now on display at Texas A&M University. The exhibit, which is on view in the Visual Arts Gallery in the Memorial Student Center, opened on April 13 and will run until May 15, 2005.

The show will then be part of the American Chemical Society Mid-Atlantic Regional Meeting (MARM) being held May 22-25 at Rutgers.

The Art of Science traveling exhibit displays images of molecules in the PDB, including the pictures available from Structure Explorer pages and from Molecule of the Month features. Since its beginnings at a space dedicated to art exhibits at Rutgers University, the show has travelled to EMBL-Hamburg, Germany; University of Wisconsin-Madison; California State University, Fullerton; Purdue University; and Hyderabad, India. The RCSB PDB would like to see the "Art of Science" travel to other places. If you would be interested in sponsoring this exhibit at your institution, please let us know at info@rcsb.org.

12-Apr-2005

RCSB PDB Focus: Help desks for beta site feedback, deposition information, and more

For answers to questions ranging from "how can I deposit my structure" to "how can I create a report about the structures I've found" to "what is DNA?", the RCSB PDB actively maintains several e-mail help desks. Responses to requests sent to these help desks are rapidly returned.

* betafeedback@rcsb.org responds to bugs and comments sent about the beta web site that is currently undergoing testing (http://pdbbeta.rcsb.org).

* deposit@deposit.rcsb.org answers questions about the deposition and annotation process. A FAQ regarding depositing, updating and releasing files is also available (http://deposit.rcsb.org/depoinfo/depofaq.html).

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

05-Apr-2005

Our best wishes to Gary

After working for almost 20 years at CARB and NIST, and serving as a co-director of the RCSB PDB since 1998, Gary L. Gilliland has taken a position with Centocor (a subsidiary of Johnson and Johnson) in Pennsylvania.

Under Gary's leadership, the RCSB PDB team at CARB/NIST was responsible for cataloging, archiving, and preserving the legacy PDB materials that have been accumulating since the PDB was established in 1971 at Brookhaven National Laboratory. This team also distributed data CDs of PDB files worldwide and maintained an exact copy of the RCSB PDB production site which served as both a mirror site and a fail-over system. The functions formerly performed at the CARB/NIST site will now be assumed by the groups at Rutgers and UCSD/SDSC.

The transition has now been successfully completed. The entire RCSB PDB team thanks Gary and wishes him the best of luck in his new adventures in the world of macromolecular structural biology.

Ligand Search Interface
(click on image for larger size)

05-Apr-2005

Beta Site Focus: Improved Searching and Visualization for Ligands

Beta site searches can use common ligand names or the identification codes from the Chemical Component Dictionary (formerly called the HET group dictionary). These queries will search ligand names, some synonyms, and class specifications using the Chemical Component Dictionary created by curation efforts of the RCSB PDB team.

Ligand name searching supports partial string matches. For example, searching for 'benz' will return all structures that contain benzene as well as those containing benzamidine. For an exact match, complete name of the ligand must be entered. Ligand searches can also be performed using the three character ligand ID in the PDB file (the "HET" record). For example, searching for 'HEM' returns all structures that have a heme ligand.

A recently added search feature is the ability to query for ligands using a SMILES string representation or a 2D structure of the ligand drawn using the MarvinSketch applet. SMILES is an acronym for Simplified Molecular Input Line Entry Specification. It is a comprehensive yet simple nomenclature system for chemicals. A SMILES string represents the valence model of a molecule.

For example, [Fe+2] or [Fe++] is the SMILES string for iron(II) cation; C1=CC=CC=C1 or c1ccccc1 is the SMILES string for benzene; and Nc1ncnc2n(cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O is the SMILES string for Adenosine-5'-triphosphate

Exact, substructure, and similarity searches can be performed. An exact search will retrieve PDB IDs associated with ligands whose structures match the SMILES/2D structure exactly. A substructure search will retrieve all PDB IDs associated with ligands that are superstructures of the query. A similarity search returns PDB IDs associated with ligands whose topology is similar to that of the query.

Similarity searches are based on finding molecules similar to the query based on dissimilarity co-efficient, whose value can be set to range from 0 to 1. The default value is 0.3. The dissimilarity coefficient is defined as 1-Tanimoto Coefficient. The higher the value, the greater the hits, since ligands that are only remotely similar to the query are also returned. A lower threshold returns fewer hits. It is more stringent in that it returns ligands that have greater similarity to the query structure.

Both the SMILES string search and the 2D structure search list all the ligands that match the query and the criteria. The matching ligands can be viewed and further explored. A 2D ligand viewer can also be launched from the Structure Explorer page for a single structure. For example, an exact search for the SMILES string for ATP, 'Nc1ncnc2n(cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O' returns all structures containing ATP. Clicking on one of the results opens up the Structure Explorer page. The user can click on the 'View' link in the 'Chemical Component'->'View Ligand' section of the page. The resulting 'Ligand Summary' page lists information pertaining to the ligand. The user can download the mol file, retrieve all structures with the ligand by clicking on the HET ID or run a SMILES string search by clicking on the same from the Ligand Summary page.

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

29-Mar-2005

RCSB PDB Education Activities: ASBMB and NSTA

Members of the RCSB PDB will be participating in a variety of upcoming education-based meetings.

  • RCSB PDB materials will be distributed at the National Science Teachers Associations National Convention (March 31 - April 3, Dallas, TX) as part of the MSOE Center for Biomolecular Modeling's exhibit booth (634). RCSB PDB member Christine Zardecki will be on hand to meet with science teachers from around the country.
  • A Symposium entitled "The Protein Data Bank in the Classroom and Beyond" will be part of the Education in the Biomolecular Sciences: The Next Generation Meeting symposium held as part of the American Society for Biochemistry and Molecular Biology's (ASBMB) Annual Meeting (April 2-6, San Diego, CA). The RCSB PDB will also be exhibiting in booth #1311 at this meeting.

22-Mar-2005

Status Report on "Large Macromolecular Complexes in the Protein Data Bank" Published

An overview of the large complexes in the PDB and some of the challenges experienced in their representation, visualization, analysis, and archiving has been published.

Large Macromolecular Complexes in the Protein Data Bank: A Status Report
Shuchismita Dutta and Helen M. Berman
Structure, Vol 13, 381-388, March 2005
http://www.structure.org/cgi/content/abstract/13/3/381

15-Mar-2005

ASBMB Meeting: RCSB Exhibit Booth and Education Symposium

The RCSB PDB be will participating in the American Society for Biochemistry and Molecular Biology's (ASBMB) Annual Meeting (April 2-6, San Diego, CA), which is being held in conjunction with the Experiemental Biology conference.

* A Symposium entitled "The Protein Data Bank in the Classroom and Beyond" is part of the Education in the Biomolecular Sciences: The Next Generation Meeting. On Wednesday morning (April 6), the following presentations will be made:

Using the new RCSB PDB web site in teaching structural biology

Phil Bourne, University of California, San Diego

From cyberspace to real space: Enhancing molecular visualization tools with physical models of proteins

Timothy Herman, Milwaukee School of Engineering

Learning about life through structures: How RCSB-PDB can help you

Shuchismita Dutta, Rutgers University

Exploring the PDB

David Goodsell, The Scripps Research Institute

Protein folder, a protein model-building kit

Richard Garratt, University of Sao Paulo, Brazil

Judith Flippen-Anderson of the RCSB is the chair of the session.

* Demonstrations of the beta site will be available from the RCSB PDB Booth (#1311) in the Exhibit Hall.

The exhibit will be open Sunday and Monday (April 3-4) from 9:00 AM - 4:00 PM and Tuesday (April 5) 9:00 AM - 3:30 PM. We hope you stop by and say hello!

08-Mar-2005

Physical Model of February's Molecule of the Month - Major Histocompatibility Complex - Available on Loan to Educators

As part of a project by Molecule of the Month author David S. Goodsell (The Scripps Institute) and Tim Herman (Center for BioMolecular Modeling), a physical model of Class I MHC is available on loan to educators. This study will explore how physical models can be used to enhance the value of the online Molecule of the Month teaching resource. The models may be borrowed for a period of two weeks. The only cost involved is for return shipping. Further information about this opportunity is available at http://www.rpc.msoe.edu/cbm/borrow_mhc.php.

01-Mar-2005

Beta Site Focus: Query-by-Example in Structure Explorer Pages

The Structure Explorer page for any PDB entry can perform several "query-by-example" searches. Using the information available in a particular entry, structures containing the same data can be quickly found by clicking on that data item.

For example, all other entries by a specific primary citation author can be found by clicking on the author's name. A search of the database for all structures in which the selected author appears in the citation will be presented in a Query Results Browser.

Authors, Primary Citation Authors, Chemical Components, and GO, CATH, and SCOP classifications can all be used in "query-by-example" searches.

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

Crystal structure of a protein
with unknown function
from Leishmania major,
a parasite of the human
immune system (PDB ID: 1XN4)

01-Mar-2005

Structural Genomics Focus: NIGMS Project Yields More Than 1,000 Protein Structures

The Protein Structure Initiative (PSI), a national program aimed at determining the three-dimensional shapes of a wide range of proteins, has now determined more than 1,000 different structures. These structures will shed light on how proteins function in many life processes and could lead to targets for the development of new medicines.

The full story from the National Institute of General Medical Sciences is available from http://www.nigms.nih.gov/news/releases/021005.html.

22-Feb-2005

Time-stamped Copies of PDB Archive Available via FTP

Starting with January 2005, time-stamped yearly snapshots of the PDB Archive will be available from ftp://snapshots.rcsb.org/. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

Currently, the directory 20050106 is available. This directory contains the exact and complete contents of the FTP archive as it appeared on January 6, 2005. This includes the 29040 experimentally-determined coordinate files that were current (i.e., not obsolete) in PDB and mmCIF formats. Data in XML (PDBML) format are not included in this first snapshot, but will be made available on DVD in the near future. Subsequent snapshots on this FTP server will include data in PDB, mmCIF, and PDBML formats.

The snapshot follows the historical directory structure -- coordinate files are contained in subdirectories named after the two middle characters of the PDB ID, for example, 100d is found in the directory '00'.

The date and time stamp of each file indicates the last time the file was modified. Entries in the PDB archive have been processed by the three members of the wwPDB (RCSB, MSD-EBI, and PDBj).

22-Feb-2005

Art and Science Events Unfurl...

Several intersections between art and science have recently been coming into play.

  • Juried Art/Science Competitions
    A juried exhibition of art related to crystallography will be held during the IUCr meeting in Florence (Information is available at http://www.iucr2005.it/exh_art_cry.htm). The ACA Newsletter is also sponsoring an Art in Crystallography competition for images to be displayed at the ACA meetings and in their newsletter. For more information, please contact the editor Connnie Chidester at ConnieChidester@earthlink.net.
  • The Gates
    Members of the PDB community have been interested in Christo and Jeanne-Claude's art installation The Gates Central Park, New York 1979-2005 . The New York Times captured depositor Wayne Hendrickson and his daughter watching the unfurling of the Gates, and RCSB team member Christine Zardecki participated in the installation of The Gates in the park.
  • RCSB PDB's Art of Science Traveling Exhibit
    The RCSB PDB's own Art/Science show is preparing to go on the road again. The exhibit uses images from the RCSB Protein Data Bank to show the beauty inherent in the three-dimensional structures of proteins. Various representations of proteins found in the PDB are highlighted, including large scale depictions of the images available from RCSB PDB Structure Explorer pages and pictures from the PDB's Molecule of the Month series by David S. Goodsell.
    The show will be part of the American Chemical Society's Mid-Atlantic Regional Meeting (MARM; May 22-25, 2005; Rutgers, University).
    The Art of Science show has already been on display at gallery spaces around the world, including Rutgers University, EMBL-Hamburg (Germany), University of Wisconsin-Madison, California State University, Fullerton, Purdue University, Hyderabad (India), and Farleigh-Dickinson University. For more information about this exhibit, please contact info@rcsb.org.

15-Feb-2005

PDB Focus: Weekly Deadlines for Release/Modify Entry Requests

PDB entries are processed by the three members of the wwPDB (RCSB, 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 PDB staff 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 update, any required author correspondence should be sent to the appropriate wwPDB member by the following times:

  • RCSB (deposit@deposit.rcsb.org): 15:00 EST Friday
  • MSD-EBI (pdbhelp@ebi.ac.uk): 15:00 GMT Thursday (10:00 EST Thursday)
  • PDBj (adit@adit.protein.osaka-u.ac.jp): 13:00 JST Thursday (23:00 EST Wednesday)

All entries due for release are transferred to the RCSB 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.

08-Feb-2005

RCSB PDB Exhibit at the Biophysical Society Meeting

The RCSB PDB will participate in the exhibition at the 49th Annual Meeting of the Biophysical Society (February 12-16, 2005 in Long Beach, California). Staff will be available at booth #538 to answer questions and to demonstrate this beta site. We hope to see you there!

An example of a customized report
(click on image for larger size)

01-Feb-2005

Beta Site Focus: New Customizable Tabular and Structure Reports

Customizable reports are now available as a new feature on this beta site. Users can select specific data items to display for individual structures or for a group of structures. These reports can be saved in a CSV format that can be opened in any spreadsheet application program.

Individual customizable reports can consolidate information from the four major areas of the "Summarize" pulldown menu found on the 'Structure Explorer' page (Biology and Chemistry, Materials and Methods, Sequence Details and Structural Features). The report also can display information specific for the type of the experimental method (X-Ray and NMR). In addition, the report can also provide ligand details, SCOP and CATH classifications, and the primary citation. An option to generate a custom structure report can be found in the pulldown menu on the 'Structure Explorer' page for a single structure. These reports include images of the asymmetric and biological units. A PDF can be viewed and saved by clicking on the 'Print Page' link in the navigation bar at the top of the page.

Reports for a set of structures can include information from a variety of areas, including Sequence, Ligands, Biological Details, and Experimental Details. After selecting the set of structures, these reports can be generated by using the "Customize Report" option from the "Report" pulldown menu on the 'Query Results Browser' page. The report generated can be sorted in ascending/descending order of any column by clicking on the column headers.

Comments and suggestions about the beta site are welcomed at betafeedback@rcsb.org.

25-January-2005

Winter Newsletter Published: A Look at 2004 Depositions, Early Protein Structures, Beta Site Features, and More

The Winter 2005 issue of the RCSB PDB Newsletter has been released in HTML and PDF formats. Highlights 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 beta site features, and summarizes statistics about structures deposited to the PDB in 2004.

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 here.

18-Jan-2005

PDB Focus: Changes and Corrections to Entries in the PDB Archive

PDB users wishing to contribute corrections to entries in the PDB archive should send this information to deposit@deposit.rcsb.org.

Corrections to entries originally processed by the RCSB, EBI-MSD, or PDBj are handled by the same annotation staff and subsequently reviewed by the author(s) depositing the structure. Any changes in released PDB entries are described in the PDB REVDAT records and in the mmCIF/XML category DATABASE_PDB_REV_RECORD categories.

When replacement coordinates for a released entry are provided by the depositing author, the original entry is obsoleted and the replacement coordinates are released in a new superseding PDB entry. The relationship between obsolete and superseding entries is stored in OBSLTE/SPRSDE PDB records and in the mmCIF/XML category PDBX_DATABASE_PDB_OBS_SPR. Queries of obsoleted entries on the RCSB PDB website always produce the most recent superseding entry. Obsoleted entries remain available in a separate area of the PDB ftp site, ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/.

For the entries deposited prior to 1998, a variety of consistency checks have been performed. This has been done as part of an ongoing wwPDB project to maintain uniformity within the PDB archive. Examples of uniformity corrections include corrections related to atomic nomenclature for both macromolecule(s) and ligand(s), sequence-coordinate consistency, and the addition of missing records (e.g. citations, synonyms, and sequence database references). Data uniformity efforts by MSD-EBI and PDBj will be incorporated into these data in the near future.

Corrections in the pre-1998 entries have been made only in the mmCIF and XML data files. The mmCIF and XML data files are offered as download options on the RCSB PDB website and are also available via ftp.

The XML data files were produced as part of a joint project by all wwPDB members, and these files are in the final stage of beta testing. Both mmCIF and XML data files conform to the PDB Exchange data dictionary. This dictionary is available in both mmCIF and XML schema form at http://deposit.pdb.org/mmcif/.

11-January-2005

2004 Deposition Statistics

In 2004, 5356 experimentally-determined structures were deposited to the PDB archive -- a 14.5% increase over 2003's 4677 depositions.

The entries were processed by wwPDB teams at RCSB-Rutgers, MSD-EBI, and PDBj. Of the structures deposited in 2004, 76% were deposited with a release status of "hold until publication"; 14% were released as soon as annotation of the entry was complete; and 10% were held until a particular date.

83% of these entries were determined by X-ray crystallographic methods; 14% were determined by NMR methods. 78% of these depositions were deposited with experimental data.

04-January-2005

PDB Data Distributed on CD-ROM and DVD in 2005

For 2005, the RCSB will distribute data to subscribers on DVD or CD-ROM each quarter.

The two-DVD quarterly sets will contain all structural and experimental data available in the archive at that time. The same data set on CD-ROM would require 20 disks.

The CD-ROM quarterly sets will contain structures released or modified during the previous three months.

Further details and ordering information are available here.

Orders received after production has begun (January 7, April 8, July 8 or October 7, 2005) will be added to the next quarterly production cycle. Questions should be directed to pdbcd@rcsb.org.

04-January-2005

RCSB Beta Site Focus: Detailed Help System

RoboHelp

This beta site uses the integrated system RoboHelp to offer detailed guidance for navigating the site and understanding the information available from the RCSB PDB. RoboHelp organizes all the help pages on the site and offers a table of contents, index, and glossary on every RoboHelp page. These tools help users to access the rich content offered by the help pages.

The help system launches into a separate browser window to allow users to access the help information and the beta site at the same time. Once users are in the RoboHelp system, they can access help on specific topics by browsing through the table of contents in the left hand menu. These topics include Getting Started, Deposit Data, Validate Data, Download Files, FTP Server, Search/Browse the Database, Query Results Browser, and Viewing Molecules.

The Help link located at the top of the home page launches the system. Links to specific help features and topics (such as "How to Validate Data", "How to Search", and "Molecular Viewer Help") are located in the left hand navigation bars, menus and pages throughout the website. An introduction to using RoboHelp on the beta site is available.

The Glossary offered by the help system provides definitions for terms related to structural biology, and is an excellent source of information.