2008 PDB News
Contents:
Earlier news is available and is archived in the RCSB PDB newsletters.
Image of green fluorescent protein was created by David S. Goodsell using the Python Molecular Viewer (mgltoools.scripps.edu). Structure shown is PDB ID 1gfl (F. Yang, L.G. Moss, G.N. Phillips Jr. (1996) The molecular structure of green fluorescent protein. Nat.Biotechnol. 14: 1246-1251).
30-December-2008
Happy Holidays
Best wishes for a happy holiday season and a wonderful new year! 2008 highlights have included the release of the 50,000 structure in the archive and the 100th Molecule of the Month; the educational Looking at Structures feature; resources for deposition, such SF-Tool for structure factor files; website tools like the enhanced RSS feed and a browser compatability check; and the wwPDB's publication of the Comprehensive Format Guide Version 3.2.
For even more developments, check out the 2008 RCSB PDB Annual Report (PDF).
23-December-2008
Looking at Structures: A Resource for Learning About PDB Data
Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file? These questions and many others are explored in the RCSB PDB's new Looking at Structures.
Using text, images, and interactive Jmols, Looking at Structures intends to help researchers and educators get the most out of the PDB archive. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive.
A Table of Contents appears on the right side of every page so at any time users can access the individual pages: Biological Units, Dealing with Coordinates, Methods for Determining Structure, Missing Coordinates and Biological Units, Molecular Graphics Programs, Resolution, and R-value and R-free.
Looking at Structures is available from the General Education section of the left-hand menu.
Currently Available Job Openings
The RCSB PDB is currently looking for new people to join our team. Available positions include a Java Developer, a Scientific Software Developer and a System Administrator.
For more details, please see the RCSB PDB Job Listings page.
A milestone was reached in April 2008 when the 100th installment of the Molecule of the Month was published on adrenergic receptors. This report cover highlights structures published in this series since January 2000.
16-December-2008
2008 Annual Report
The 2008 Annual Report (PDF) highlights current progress and accomplishments, and explores the RCSB PDB's different activities in data deposition, query, and education. This publication is currently being distributed to the diverse community of PDB users in academia, industry, and education. If you would also like a printed copy, please send your postal address to [email protected].
02-December-2008
Announcement: PDB Archive Version 3.15 to be Released
A new standardized version of the PDB archive will be available from ftp://ftp.wwpdb.org in early 2009. All entries released prior to December 2, 2008 will be re-released as PDB Format Version 3.15 files. This release will overwrite all existing files. A snapshot of the archive before this release will be available from https://snapshots.wwpdb.org/.
For documentation, please see www.wwpdb.org/docs.html
Questions may be sent to [email protected].
25-November-2008
Announcement: New Releases to Follow Format Guide Version 3.20
Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version 3.20 (PDF | HTML). This format includes site and assembly annotation, and supports the nomenclature introduced in 2007 in the Chemical Component Dictionary. The Version 3.20 Changes Guide highlights the lists changes in format from 3.1.
Please send any questions to [email protected].
18-November-2008
2D and 3D representations of sequence and domain annotations PDB entry 1cdg (Click image to enlarge)
View Domain Annotations in 3D
Sequence Details pages for all protein structures now include a Jmol view of the structure that can display domain annotations from SCOP, CATH, DP, PDP, Pfam, and InterPro.
To activate this view from a structure summary page, first select the Sequence Details tab. The default view displays a 2D graphical representation of the UniProt, PDB-ATOM and PDB-SEQRES sequences. Users can also select third-party domain annotations from this 2D image to appear to the corresponding structure in a Jmol viewer.
To view these annotations mapped onto the 3D structure, select [show 3D in Jmol] from the top of the page. Then, click on any of the domains on the sequence view. The corresponding colors for that domain will appear in the 3D Jmol viewer. The annotations shown in Jmol can change by clicking on an annotation shown in the 2D view.
By default, the Jmol window stays positioned on the top of the page. Select [dynamic Jmol position] to have the Jmol viewer adjust so that it is always to the top right of the page as you scroll down.
News and Publications
11-November-2008
Focus: News and Publications
Interested in an older Education Corner from the Newsletter? Want to know what papers have been published that discuss the project? Looking for a flyer to guide you through the deposition process? The News and Publications page offers access to all RCSB PDB publications. Located in the General Information section of the left-hand menu, this page archives our Annual Reports that describe the history, mission, and accomplishments of the project; Publications in peer-reviewed journals; weekly News about new features and events; the quarterly Newsletter; and more.
To request printed versions of any of these documents, please send your mailing address to [email protected].
04-November-2008
Tips for Depositing Multiple Related Structures using ADIT/ADIT-NMR
- Use pdb_extract when preparing structures solved using X-ray crystallography or NMR. Not only does pdb_extract minimize the amount of manual typing needed during the deposition process, it also utilizes an "author information form" that can be filled out once for use with multiple entries.
- For structures solved by other experimental methods, deposit one representative structure. After it has been annotated and processed, use this finalized entry as a template for the related depositions by replacing the coordinates and updating information in the PDB or mmCIF file as necessary.
- If the structures have bound ligands, drugs, or inhibitors, please check Ligand Expo for matching chemical components. If a match is found, use that corresponding ID code for the component in your coordinates. If a match is not found, choose a new three-character code for the component, and upload the chemical name and a file showing the chemical drawing for the new component into the Ligand Information section of ADIT/ADIT-NMR.
When depositing many structures that are related to one another, there are a few ways of making the ADIT/ADIT-NMR deposition process simpler:
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/ADIT-NMR.
The "author information form" contains author names, citation information, protein names and source--the types of information that are repeated in multiple related entries. This form can be filled out once and used with pdb_extract to prepare several structures for deposition.
28-October-2008
Fall 2008 RCSB PDB Newsletter
Fall 2008 RCSB PDB Newsletter Published
The Fall edition of the RCSB PDB Newsletter (HTML | PDF) describes how Ligand Expo can be used to deposit structures, and announces the Comprehensive Format Guide for the PDB File Format (Version 3.2). Other highlights include the enhanced RSS feed for PDB structures and searches based on PubMed abstracts at the RCSB PDB website.
The origin and applications of the iPhone program Molecules is described in this quarter's Education Corner by Brad Larson (Sunset Lake Software).
In the Community Focus, Paul D. Adams (Lawrence Berkeley Laboratory) discusses PHENIX, the Technology Port of the PSI Structural Genomics Knowledgebase, and his work at the Joint BioEnergy Institute.
If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to [email protected].
Subscription information for the plain text electronic version is also available.
21-October-2008
RSS Feed
Symbol
Enhanced RSS Feed from the RCSB PDB
The RCSB PDB offers an RSS (Really Simple Syndication) feed that provides users with a list of newly updated structures as soon as they are released. Based upon user feedback, this weekly feed now includes each PDB ID and structure title. Subscribers to this feed can quickly scan the list for structures of interest.
To start, select an RSS reader. Many RSS feed readers are already packaged with web browsers and email programs, while others are available as dedicated programs or websites.
To incorporate the RCSB PDB feed, either drag or select the orange RSS icon from the top of the RCSB PDB home page (located just next to the latest release date) and add the URL for new structures to your reader.
Green Fluorescent Protein (GFP)
14-October-2008
Nobel Prizes and the Molecule of the Month
Congratulations to the awardees of the 2008 Nobel Prize in Chemistry for the discovery and development of the green fluorescent protein (GFP)--Osamu Shimomura (Marine Biological Laboratory, Woods Hole, MA and Boston University Medical School), Martin Chalfie (Columbia University), and Roger Y. Tsien (University of California, San Diego).
To learn more about GFP from a molecular point of view, the June 2003 Molecule of the Month feature discusses its structure and function. Exploring the Bioinformatics of Green Fluorescent Protein is a tutorial that uses visualization tools from the RCSB PDB website to examine this protein.
07-October-2008
Chaille T. Webb, Poster Prize winner at IUCr
RCSB PDB Poster Prize Awarded at IUCr Meeting
The RCSB PDB Poster Prize for best student poster related to macromolecular crystallography at the XXI Congress & General Assembly of the International Union of Crystallography (IUCr; August 23 - 31 in Osaka, Japan) was awarded for
"Structural insights into the mitochondrial import complex, TIM9.10" by Chaille T. Webb,1,2 Michael Baker,1 Michael T. Ryan,1 Peter M. Colman,1 and Jacqueline M. Gulbis1
(1The Walter and Eliza Hall Institute of Medical Research and
2The University of Melbourne, Australia)
Webb will receive a subscription to Science and a copy of the International Tables for Crystallography.
Thanks to all of the participating students and the judging committee.
30-September-2008
Exploring Structures Through PubMed Abstracts
PubMed abstracts for the primary citations of PDB entries are integrated with the RCSB PDB website.
For query results of multiple structures, the Citations Tab provides a PubMed-like list of the corresponding primary citations. This list can be downloaded in Medline format for use with bibliographic programs such as Endnote and RefWorks by selecting the "Medline Format" option from the lefthand menu. The Citations Tab also links to all structures that share a primary citation, and to related articles in PubMed.
For each PDB structure, the "Abstract" link on a Structure Summary page provides information downloaded from PubMed about the citation. The keywords, title, and abstract on this page can be used to query the PDB for other entries that have the same words in their abstracts. The citation information can be downloaded in Medline format by selecting the "Medline Format" option from the lefthand menu. Selecting the PubMed icon takes users to the abstract in PubMed.
Using the Advanced Search, PubMed keyword searches can be combined with any other query option.
23-September-2008
Ligand Expo: A Resource for Depositing Structures
The Chemical Component Dictionary archives chemical and structural information about all residue and small molecule components found in PDB entries. Ligand Expo is a new tool that can access, visualize, and build reports about these data. It can also be used to prepare a file for deposition:
- Search Ligand Expo for a chemical component that matches your ligand
- If a match is found, use that corresponding three-letter code for the ligand in your coordinates
- If the ligand is not found, choose a new three-letter code for the ligand
- When depositing your structure with ADIT, upload the chemical name and a file showing the chemical image for the new ligand into the Ligand Information section
Ligand Expo capabilities have been described online and in a flyer available for download.
16-September-2008
Announcement: Comprehensive Format Guide Version 3.2
During the past year, the wwPDB annotators have collaborated on a project to clarify the details and procedures related to data processing and annotation. The result is a PDB Contents Guide Version 3.2 that more fully describes the PDB file format. This document is available as a PDF and in HTML, and is accompanied by a document highlighting these clarifications.
In the coming months, all files released by the wwPDB will follow the format as described in this document. Details will be made available on this website and at www.wwpdb.org.
09-September-2008
Upcoming wwPDB Presentations
The wwPDB and related resources will be discussed at several meetings in September. In addition to the wwPDB Advisory Committee meeting to be held on September 29, the following presentations will be made:
- At the International Structural Genomics Organization's Conference on Structural Genomics (Sept. 20-24; Oxford, UK), RCSB PDB Director Helen Berman will describe the PSI Structural Genomics Knowledgebase, a resource that provides integrated access to all PSI products, including the structures found in the PDB archive.
- At the EMBO 08 Practical Course on Computational Aspects of the Protein Target Selection, Protein Production Management and Structure Analysis Pipeline (Sept. 22-26; Hinxton, UK), Helen Berman and John Westbrook (RCSB PDB), Haruki Nakamura (PDBj), and Kim Henrick, Dimitris Dimitropoulos, Eugene Krissinel, and Tom Oldfield (PDBe) will discuss various resources and tools.
- At the European Conference in Computational Biology (ECCB08; Sept. 22-26; Sardinia, Italy), Martha Quesada (RCSB PDB) will describe the multifaceted wwPDB collaboration and highlight features found at the RCSB PDB, PDBe, PDBj, and BMRB websites.
Detailed information about the wwPDB is also available at www.wwpdb.org.
02-September-2008
RCSB PDB Poster Prize Awarded at ISMB Meeting
The RCSB PDB Poster Prize for best student poster related to structure and function prediction at the 16th Annual International Conference on Intelligent Systems for Molecular Biology (July 19-23, 2008; Toronto, Canada) went to Dariya Glazer for "Clustering Across Space and Time" (Dariya Glazer, Randy Radmer, Russ Altman, Stanford University).
Glazer will receive a subscription to Science and a reference book.
Thanks to everyone who participated, especially our judges: Marco Punta (Committee Chair), Yana Bromberg, Columbia; Matteo Dal Peraro, Ecole Polytechnique Federale de Lausanne; Claudia Dall'Armi, Columbia; Marco DeVivo, Rib-X Pharmaceuticals, Inc.; Zsuzsanna Dosztanyi, Markus Fischer, Laszlo Kajan, Andrew Kernytsky, Rajesh Nair, Avner Schlessinger, Ta-tsen Soong, Columbia University; and the International Society for Computational Biology, particularly Steven Leard.
PDB Focus: What is the smallest polymer structure that can be deposited to the PDB?
The PDB contains biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes.
Polypeptide structures containing 24 or more residues can be deposited to the PDB. Smaller peptides that are complexed with a larger polymer (greater than the minimum length defined above) may be deposited to the PDB. Crystal structures of peptides with fewer than 24 residues, such as antibiotics, should be sent to the Cambridge Crystallographic Data Centre (CCDC).
Polynucleotide structures with 4 or more residues are accepted at the PDB. Smaller oligonucleotides (dinucleotides and trinucleotides) can be deposited at the Nucleic Acid Database (NDB).
Coordinates for the repeating unit of fibrous polymers and polysaccharide structures with 4 or more sugar residues may be deposited at the PDB archive. Molecules that do not conform to these guidelines but have been previously deposited in the archive will not be removed.
Structures may be deposited to the archive via the worldwide Protein Data Bank.
26-August-2008
Download Statistics Available by Structure ID
Downloads from the PDB archive are one of the primary means of accessing scientific structure results. While there are cross-links between the corresponding scientific publication and the PDB entry, in many cases it is the structure file that is accessed and downloaded more frequently.
The wwPDB website has recently added statistics for FTP and HTTP (web) downloads and views for each PDB structure. The high volume of data downloaded around the world underscores the importance of including informative, accurate, and annotated PDB data in the archive. Data are available by month, starting from August 2007, for each wwPDB site. These statistics can be accessed a number of ways:
- A searchable database can be searched by ID or group of IDs. Results can display the wwPDB site and month accessed, and include a line chart illustrating FTP and HTTP activity over time.
- Tables provide full and summary statistics. The summary table offers an overall view of activity. For example, 18,051,769 FTP downloads and 4,122,104 HTTP downloads/web page views were made across all wwPDB sites in July 2008. Full Download Complete Reports can be downloaded in CSV and TAB formats.
- The Top 10 Download Statistics page offers a quick look at structures being downloaded by the most recent month and overall since August 2007. For example, 1crn was the #1 structure viewed and downloaded via HTTP from August 2007 - June 2008. In this table, mouse over the PDB ID to view the structure title.
All download statistics are updated monthly, and collected on an aggregate, rather than individual, basis. The wwPDB does not share server log information with third parties for marketing or other purposes.
To access these features, select Statistics>Downloads from the top menu bar at www.wwpdb.org. The wwPDB website also offers links to member sites, documentation, news, and deposition and processing statistics. Questions may be sent to [email protected].
19-August-2008
IUCr: wwPDB Exhibition Stand and Presentations
The wwPDB partners will be exhibiting at the XXI Congress & General Assembly of the International Union of Crystallography (IUCr; August 23 - 31 in Osaka, Japan) at booth #14. Please stop by for website demonstrations and to meet with wwPDB members from around the globe.
RCSB PDB Director Helen M. Berman will present a keynote lecture entitled "What the Protein Data Bank tells us about the past, present, and future of structural biology" on Sunday August 24.
On Saturday, August 30, John Westbrook will present "Data Quality in the PDB Archive".
The RCSB PDB Poster Prize will be awarded to the best student poster at the meeting and announced at the awards ceremony. To participate, please place the RCSB PDB sticker available at the meeting onto your poster.
12-August-2008
DOIs for PDB Structures and the Molecule of the Month
PDB structures can be cited using their PDB ID and the related published citation.
Structures may also be referenced using their Digital Object Identifier (DOI). These DOIs are formatted as 10.2210/pdbXXXX/pdb - where XXXX is the PDB ID. For example, the DOI for entry 4HHB is "10.2210/pdb4hhb/pdb".
This DOI can be used in a URL (http://dx.doi.org/10.2210/pdb4hhb/pdb) or entered in a DOI resolver (such as http://www.crossref.org/) to automatically link to pdb4hhb.ent.Z in the main PDB FTP archive.
DOIs are also available for each RCSB PDB Molecule of the Month feature with the format: 10.2210/rcsb_pdb/mom_YYYY_MM (where YYYY is the year, and MM the number of the month, one or two digits). For example, the DOI for the May 2003 feature on hemoglobin by Shuchismita Dutta and David S. Goodsell is "10.2210/rcsb_pdb/mom_2003_5". An RCSB PDB Molecule of the Month feature may be referenced using the DOI and the author/s of the article.
A page describing policies & references for using and citing PDB data and RCSB PDB resources is available.
05-August-2008
ADIT Focus: Session Restart IDs
A structure can be deposited over a period of time 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 deposition session. 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 both the PDB and BMRB.
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.
29-July-2008
Summer 2008 RCSB PDB Newsletter Published
The Summer edition of the RCSB PDB Newsletter (HTML | PDF) highlights new deposition tools, such as SF-Tool and Ligand Expo, and explores usage statistics for PDB data. The New Jersey and National Protein Modeling events at the Science Olympiad are described, along with recent presentations and publications.
In this quarter's Education Corner, Judy Voet (Swarthmore) and Donald Voet (University of Pennsylvania) discuss Biochemistry and Molecular Biology Education (BAMBED), a Journal for University, College, and High School Educators.
John Norvell (NIGMS) discusses his career, NIGMS, and the Protein Structure Initiative.
If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to [email protected].
Subscription information for the plain text electronic version is also available.
22-July-2008
wwPDB Paper: Representation of viruses in the Remediated PDB
The 2007 release of remediated data improved the representation of deposited and experimental coordinate frames, symmetry, and frame transformations in the archive. A paper describing the scheme used by the wwPDB to represent viruses and other biological assemblies with regular noncrystallographic symmetry has been published:
Acta Cryst. (2008). D64, 874-882 [ doi:10.1107/S0907444908017393 ]
Representation of viruses in the remediated PDB archive
C. L. Lawson, S. Dutta, J. D. Westbrook, K. Henrick and H. M. Berman
15-July-2008
RCSB PDB at ISMB, Protein Society Meetings
Stop by exhibit booth #19 at the 16th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB) to visit with the RCSB PDB (July 19-23; Toronto, Canada). Also at this meeting, the RCSB PDB Poster Prize will be awarded for the outstanding student poster in the "structure and function prediction" category. Associate Director Phil Bourne will be involved with presentations and discussions, including a 3DSig Keynote Lecture at the Structural Bioinformatics and Computational Biophysics satellite meeting.
At the 22nd Annual Symposium of The Protein Society (July 19-23; San Diego, CA), Peter Rose will present the poster "Effective Mining of the Protein Data Bank".
Other upcoming meetings include presentations and a wwPDB exhibit booth at the XXI Congress and General Assembly of the International Union of Crystallography (August 23-31; Osaka, Japan).
08-July-2008
Notice: Planned SDSC Power Outage July 8-9
The San Diego Supercomputer Center (SDSC) hosts servers used by the RCSB PDB. On July 8-9, 2008, SDSC will perform necessary repairs and maintenance on an electrical transformer.
We anticipate providing uninterrupted service during this time through off-site failover servers located at the Skaggs School of Pharmacy and Rutgers University for the following resources:
- RCSB PDB production website (www.pdb.org)
- RCSB PDB production FTP site (ftp://ftp.wwpdb.org)
- Snapshots FTP site (ftp://snapshots.rcsb.org)
- wwPDB website (www.wwpdb.org)
RCSB PDB deposition services will not be affected. The update to the website and FTP site will proceed as scheduled.
The following services will NOT be available during this time:
- Beta RCSB PDB website (betastaging.rcsb.org)
- The retired FTP site (ftp.rcsb.org)
Email sent to [email protected] and RCSB PDB members with an sdsc.edu address will be queued and delivered after the maintenance has been completed.
24-June-2008
Ligand Expo: A Small Molecule Resource
The Chemical Component Dictionary archives chemical and structural information about all of the small molecules found within PDB structure entries. Ligand Expo (ligand-expo.rcsb.org) is a new tool that can access, visualize, and build reports about these data.
With Ligand Expo, users can also
- Search for a chemical component
-
Browse tables of components that contain
- modified amino acids and nucleotides
- popular drugs (trade and generic names)
- common ring systems
- Review related information in chemical dictionaries and resource files (chemistry, geometry, atom nomenclature, and more)
- Download model and ideal chemical component coordinates
- View all instances of a component in released PDB entries
Ligand Expo is an update of the Ligand Depot resource.
17-June-2008
Wei Yong, RCSB PDB Poster Prize winner at ACA
RCSB PDB Poster Prize Awarded at ACA Meeting
The RCSB PDB Poster Prize for best student poster related to macromolecular crystallography at the American Crystallographic Association's Annual Meeting (May 31 - June 5, 2008; Knoxville, TN) went to Wei Yong for "X-ray crystallographic studies of pig sarcosine dehydrogenase" (Wei Yong, Ila Misra, Jung-Ja Kim, Medical College of Wisconsin).
Yong will receive a subscription to Science and an International Tables of Crystallography volume of his choosing.
Thanks to everyone who participated, especially our judges: Robert Rose (Chair; North Carolina State University); Gloria E.O. Borgstahl (Eppley Institute for Cancer Research and Allied Diseases); Antonella Longo (North Carolina State University); Robert McKenna (University of Florida); Joseph E Wedekind (University of Rochester).
The RCSB PDB Poster Prize will also be awarded this year at the 16th Annual International Conference on Intellligent Systems for Molecular Biology (July 19-23, 2007; Toronto, Canada) and the Congress and General Assembly of the International Union of Crystallography (August 23-31, 2008; Osaka, Japan).
10-June-2008
Workshop on Next Generation Validation Tools for the wwPDB
A meeting of the wwPDB X-ray Validation Task Force was held to collect recommendations and develop consensus on additional validation that should be performed on PDB entries, and to identify software applications to perform validation tasks.
The workshop was organized by Randy Read (Cambridge University), and sponsored by the RCSB PDB & PDBe. Detailed information about the workshop is available at http://www.wwpdb.org/workshop/2008/index.html.
03-June-2008
Secondary Structure Information
A plain text file containing sequence and secondary structure information in FASTA format for all structures is available from www.rcsb.org/pdb/files/ss.txt. A separate file, www.rcsb.org/pdb/files/ss_dis.txt, includes disordered regions in addition to the secondary structure.
These files, which replace analogous ones previously found in the FTP tree, are updated weekly.
(Click image to enlarge) Stop by our exhibit booth for RCSB PDB materials and demonstrations
27-May-2008
Ligand Expo, SF-Tool Demonstrations at ACA Meeting
Exhibit booth #500 at the 2008 Meeting of the American Crystallographic Association will be the place to find out about the latest RCSB PDB developments. Please stop by to see demonstrations of Ligand Expo, a new tool for exploring the small molecules found in PDB entries, and for SF-Tool, a resource for validating and translating crystallographic experimental data.
20-May-2008
(Click image to enlarge) The PDB archive is accessed worldwide via wwPDB members RCSB PDB, MSD-EBI, and PDBj.
(Click image to enlarge) The RCSB PDB website was visited 12,660 times from 1,807 cities on May 12, 2008.
RCSB PDB Usage Statistics
Approximately 140,000 unique visitors explore the RCSB PDB website at www.pdb.org each month (as identified by a unique IP address). During this period, these users download more than 500 GB (GigaBytes) of data. At the same time, about 7,000 unique visitors download more than 10 million files from the FTP site at ftp://ftp.wwpdb.org, for a total of about 2 TB (TeraBytes) of data. The PDB archive is also accessed through FTP sites supported by wwPDB members MSD-EBI and PDBj.
There were more than 100 million FTP file downloads, with peak rates of more than 10 files per second, during the six-month period that followed the August 2007 release of the archive of remediated data. In comparison, less than 10 million files were downloaded in all of the year 2000.
Visitors from 150 countries visit the RCSB PDB FTP and website. Approximately one third of all visitors are from the United States, another third from Europe, and a third from the rest of the world. Since users are accessing data from around the globe, traffic is evenly distributed over the course of 24 hours. On an average day, download rates never drop below 50% of peak daytime values.
Standard server log information, such as IP address, time spent on the site, browser type, etc., is collected and assessed on an aggregate, rather than individual, basis in order to track site statistics, data that are most popular to our visitors, performance monitoring, and troubleshooting. Studying access statistics and usage patterns helps to project future hardware needs, and aids in the design of new functionality. We also use this information for site and system security. We do not share server log information with third parties for marketing or other purposes.
13-May-2008
SF-Tool: A Tool for Crystallographic Experimental Data Validation
A streamlined, web-based tool is available for validating crystallographic experimental data. SF-Tool can be used to:
- Validate your model coordinates against structure factor data
- Easily translate your structure factor file between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, or OTHER format)
- Check for twinned or detwinned data
Documentation for this program is available. Questions, comments, and suggestions should be sent to [email protected].
06-May-2008
Spring 2008 RCSB PDB Newsletter Published
The Spring edition of the RCSB PDB Newsletter has been published in HTML and PDF formats. This issue highlights deposition tools, including a tool for converting structure factor files between a variety of formats, and two sites for depositing electron microscopy map data. The different types of statistics about data in the PDB archive are described, and recent outreach activities are detailed.
In this quarter's Education Corner, Jeramia Ory (Kings College) describes how he uses Chimera to create molecular multimedia in his classroom.
Christine Orengo (University College London) is the subject of this quarter's Community Focus. In this feature, Dr. Orengo discusses CATH, her research, and the development of The Protein Chart, a "periodic table" of proteins.
If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to [email protected].
Subscription information for the plain text electronic version is also available.
29-April-2008
Princeton High School Wins New Jersey Science Olympiad Protein Modeling State Finals
(Click image to enlarge) Princeton High School and their model of calmodulin. From left to right: Ola Hadaya, Sarah Goodman, and Asya Kosygina.
(Click image to enlarge) The models were carefully judged by RCSB PDB staff.
(Click image to enlarge) A closer look at calmodulin
(Click image to enlarge) Teams built a portion of the calmodulin structure using online resources.
The girls at Princeton High School held on to their championship title by coming in first place at the 2008 Protein Modeling event at the Science Olympiad State Finals in New Jersey for the second year in a row.
Teams from all over the Garden State presented their hand-built 3D models of a calmodulin protein, along with an abstract, to be judged by staff from the RCSB PDB. At the competition, teams built a model of a selected region of the structure using Jmol and took a written exam about the structure.
Teams used the Molecule of the Month, among other RCSB PDB resources, to help prepare for this event.
The highest ranking teams were Princeton High School (First Place), Livingston High School (Second), and West Windsor-Plainsboro High School North (Third).
Congratulations to all participating teams--there were many great models, abstracts, and responses to the written exam. Pictures of the event and rubrics used in judging are available at education.pdb.org/olympiad. Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to [email protected].
Special thanks to our judges from the RCSB PDB (Andrei Kouranov, Chenghua Shao, Irina Persikova, Jasmine Young, Jing Zhou, and Christine Zardecki (Event Supervisor)), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.
22-April-2008
Education Focus: DNA Day
"National DNA Day" is April 25. Commemorating the completion of the Human Genome Project in 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 National Human Genome Research Institute site for DNA Day offers teaching tools, a chatroom, and webcasts.
- 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".
- BBC News has compiled resources and images describing the story behind the discovery.
- 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.
- The RCSB PDB has many educational resources related to nucleic acid structure, including Molecule of the Month features on DNA, Transfer RNA, and Self-splicing RNA.
15-April-2008
Recent wwPDB Papers
Two wwPDB papers describing deposition have been recently published.
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wwPDB deposition tools, methods (including validation), and policies are described in
Data deposition and annotation at the Worldwide Protein Data Bank. Shuchismita Dutta, Kyle Burkhardt, Ganesh J. Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M. Berman (2008) in Methods in Molecular Biology, vol. 426: Structural Proteomics: High-Throughput Methods (Bostjan Kobe, Mitchell Guss, Thomas Huber, eds.), pp. 81-101. -
Issues relating to NMR depositions are discussed in
BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. John L. Markley, Eldon L. Ulrich, Helen M. Berman, Kim Henrick, Haruki Nakamura, and Hideo Akutsu (2008) J Biomol NMR 40(3): 153-155
08-April-2008
PDB Archive Contains More Than 50,000 Structures
With this week's update, the PDB archive reached a significant milestone in its 37-year history: The holdings now contain more than 50,000 current experimental structures.
The worldwide Protein Data Bank (wwPDB) has seen the archive double in size since 2004. The PDB was founded in 1971 with seven structures at Brookhaven National Laboratory. Today, the wwPDB receives approximately 25 new experimentally-determined structures from scientists each day for inclusion in the archive. More than 5 million files are downloaded from the PDB archive every month. Users include structural biologists, computational biologists, biochemists, and molecular biologists in academia, government, and industry as well as educators and students.
It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014.
The 50,000 structure mark was reached after another milestone event--the publication of the 100th edition of the Molecule of the Month.
Proteins, one of the main building blocks for living organisms, come in a variety of shapes, with the form of a protein corresponding to its function. The structures housed in the PDB demonstrate great diversity in size, complexity, and function, including:
- Insulin, the protein deficient in diabetic patients
- p53 tumor suppressor, a protein often implicated in cancer
- Anthrax toxin, the disease-causing protein made by anthrax
- Amyloid peptide, a protein implicated in Alzheimer's disease
- Influenza proteins, structures which may help scientists design medicines to combat the flu
- Prion proteins, misshapen proteins that are the cause of many diseases, including mad cow disease
01-April-2008
Molecule of the Month reaches 100
This month's feature on adrenergic receptors is the 100th installment of Molecule of the Month. Since January 2000, this series has explored the structure and function of proteins and nucleic acids found in the PDB archive such as transfer RNA, anthrax toxin, and multidrug resistance transporters. To commemorate this event, the RCSB PDB will be offering temporary tattoos of an adrenergic receptor at upcoming meetings. The feature is also available in a specially formatted PDF available for download.
Written and illustrated by David S. Goodsell (The Scripps Research Institute), the Molecule of the Month provides an easy introduction to the RCSB PDB for teachers and students. It is used in many classrooms to introduce structures to students, and is an integral part of the protein modeling event at the Science Olympiad.
The text and images are related to the featured molecule; the RCSB PDB pages link to examples of the molecule. In response to requests, a view of the highlighted structure in Jmol is included in new features to provide an interactive view of the molecule.
New Molecule of the Month features are made available from the RCSB PDB home page with the first update of each month. Alphabetical and chronological listings of past issues are provided. PDBj has recently started to translate the Molecule of the Month into Japanese.
Links to the series are also available from RCSB PDB's Structure Explorer pages. Selecting "Learn more: [M]" takes the reader to any Molecule of the Month feature related to that particular entry.
For a description of how the series is created, please see the RCSB PDB Newsletter's PDB Focus on David Goodsell.
25-March-2008
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). There is also a one-year limit on both HPUB and HOLD status after which a structure with no major issues can be released even if there is no corresponding publication.
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:
- RCSB PDB ([email protected]): 12 noon EST Thursday
- MSD-EBI ([email protected]): 12 noon GMT Thursday (8:00 EST Thursday)
- PDBj ([email protected]): 12 noon JST Thursday (22:00 EST Wednesday)
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.
18-March-2008
Using PubMed Abstracts to Search for Structures
(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 "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.
Positions Available
Available Positions with the RCSB PDB include openings at the University of California, San Diego for a Scientific Software Developer and for a Lead Web Architect.
11-March-2008
Using RCSB PDB Tools and Resources
A chapter describing the various options and procedures for querying, downloading and validating 3D structures from the RCSB PDB website was published in Current Protocols in Bioinformatics in December 2007. This is an update of the chapter with the same title that was published in 2005.
S. Dutta, H.M. Berman and W.F. Bluhm: Using the Tools and Resources of the RCSB Protein Data Bank
Current Protocols in Bioinformatics (December 2007) 1.9.1-1.9.24. doi:
10.1002/0471250953.bi0109s20
(journal subscription required for full text)
04-March-2008
RCSB PDB Celebrates Teaching and Learning
The RCSB PDB will be exhibiting at a Teaching & Learning Celebration on March 7-8 in New York City. Thousands of educators and policy makers from the Tri-State are expected to attend.
It's still not too late for educators to take our online survey. Do you use the Molecule of the Month? Teach classes? Use the RCSB PDB when working with students? Then we want to hear from you! The RCSB PDB is looking for feedback about the educational resources available from our website, and in particular, the types of educational activities and resources that are of interest to our users.
We greatly appreciate your participation in this survey. As a token of appreciation, we will send temporary tattoos of tRNA to survey respondents who send their postal address to [email protected].
26-February-2008
PDB Statistics
Which journal has published the most structures? What structures have been solved by more than one experimental method? Answers to these questions can be found by exploring the various statistics about the data in the PDB archive available by clicking the "PDB Statistics" link at the top of every page on the RCSB PDB website.
Charts, graphs, and tables related to content distribution include
- Summary Table of Released Entries: Current PDB holdings grouped by experimental method and molecule type
- Status of Unreleased Entries: A piechart that illustrates the status of unreleased entries
- Interactive histograms showing the archive by function, resolution, space group, source organism, journal, molecular weight, and enzyme classification
- Histogram showing the number of structures solved by structural genomics structures
- Table of proteins Solved by Different Experimental Methods
- Current statistics on redundancy in the archive
The growth of structures released in the PDB archive can be viewed per year, by experimental method, and by molecule type. Other graphs show the growth of unique protein classifications as defined by SCOP and CATH.
Positions Available
Available Positions with the RCSB PDB include openings at the University of California, San Diego for a Senior Scientist/Scientific Software Developer and for a Lead Web Architect.
Cycloviolacin (2007, copper-coated steel, 24" x 32" x 36")
19-February-2008
Protein Sculptures on Display at Rutgers
Sculptures and photographs by Julian Voss-Andreae are currently on display at Rutgers Student Center (New Brunswick, NJ) until February 22, 2008.
Voss-Andreae's unique sculptures are designed to tell stories about hemoglobin, collagen, and other structures essential to life.
Julian Voss-Andreae is a German-born sculptor based in Portland, He graduated from the Pacific Northwest College of Art (PNCA) in 2004 with a BFA in sculpture. While still at PNCA, Voss-Andreae developed a novel kind of sculpture based on the structure of proteins, the building blocks of life. Voss-Andreae's work has been commissioned internationally and has been highlighted in journals such as Leonardo and Science.
Photographs of Voss-Andreae's sculptures are part of the RCSB PDB's Art of Science traveling exhibit, which also features images available from the RCSB PDB website and the Molecule of the Month. For more information on hosting this exhibit, please contact [email protected].
Julian Voss-Andreae: www.julianvossandreae.com
Winter 2008 RCSB PDB Newsletter Redesigned and Published
With a sleek new format, the latest RCSB PDB Newsletter has been published in HTML and PDF formats. This issue describes a new version of ADIT that was developed to improve data accuracy and consistency, new outreach programs, and the publication of the 2007 Annual Report.
In this quarter's Education Corner, Teresa MacDonald (The University of Kansas Natural History Museum) describes edible protein models.
The Community Focus looks at this year's New Jersey Science Olympiad competition.
If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your postal address to [email protected].
Subscription information for the plain text electronic version is also available.
12-February-2008
EmDep2: Deposit EM Maps at the MSD-EBI or RCSB PDB
Electron microscopy map data can now be deposited to the EMDB using the improved web-based tool EmDep2. EmDep2 is available from the existing deposition site at the EBI in Europe and at a new deposition site at the RCSB PDB in the USA.
The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files.
This improvement to EMDB services is the first product of a collaboration beween the European Network of Excellence 3D-EM (http://www.3dem-noe.org/) and the recently NIH-funded partnership for a Unified Data Resource for CryoEM (http://emdatabank.org) between the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics at Rutgers, and the National Center for Macromolecular Imaging at Baylor College of Medicine.
EMDB:
http://www.ebi.ac.uk/msd-srv/docs/emdb/
EmDep2 (EBI):
http://www.ebi.ac.uk/msd-srv/emdep/
EmDep2 (RCSB PDB):
http://emdb.rutgers.edu/emdep/
05-February-2008
Historical Look at the PDB Published in a Special Issue of Acta Crystallographica
The PDB archive has grown from its early beginnings in 1971 as a handwritten petition signed by crystallographers to its current status as an online biological database and resource used by a diverse community of teachers, students, and researchers in academia and industry worldwide.
This history is described in an article published in an issue of Acta Crystallographica that commemorates various milestones in the crystallographic community. Intended for a broad audience, articles in this issue describe powerful and diverse uses of crystallography, along with a look at the history of publishing by the International Union of Crystallography.
The Protein Data Bank: a historical perspective (2008) Acta Cryst. A64: 88-95. doi: 10.1107/S0108767307035623
Bridgewater-Raritan's Daniel Zhang and Amy Song with their model of the full structure of calmodulin. Their on-site model of a section of PDB entry 1cll received a perfect score.
Northern champions Tim Kunisky and Collin Stocks. Their model was enhanced with masking tape calcium ions. The team from Livingston High School also came in first place in the overall competition.
29-January-2008
Bridgewater-Raritan HS and Livingston HS Win New Jersey Science Olympiad Protein Modeling Regionals
Many models of the structure calmodulin were built by high school students for the RCSB PDB-sponsored Protein Modeling event at the Northern and Central New Jersey Science Olympiad.
This year's protein modeling competition has three components. Students first build a model of the full calmodulin structure (entry 1cll), and bring it to be impounded in the morning for judging. In this model, teams are encouraged to include additions and an abstract that help to illustrate the function of the structure.
At the event itself, teams build a portion of PDB entry 1cll with a Mini-Toober (from www.3dmoleculardesigns.com). They also answer questions about the structure, function, importance, and history of the modeled protein. For all sections of the event, students use the Molecule of the Month, the PDB file, Jmol and the Structure Explorer page for 1cll.
Detailed information about this event is available at http://education.pdb.org/olympiad/.
At the Central New Jersey Regional held at Princeton University, Bridgewater-Raritan High School came in first; South Brunswick High School, second; and West Windsor-Plainsboro High School North, third.
At the Northern New Jersey Regional held at New Jersey Institute of Technology, Livingston High School came in first; Westfield High School, second; and Bergen County Academies, third.
The state finals will take place March 11, 2008 at Middlesex County College in Edison, NJ.
Special thanks to our judges from the RCSB PDB (Shuchismita Dutta, Sutapa Ghosh, Andrei Kouranov, Irina Persikova, Monica Sekharan, Chengua Shao, Huangwang Yang, Jasmine Young, Christine Zardecki, and Jing Zhou), 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!
22-January-2008
Paper Published Describing the Scope and Methods of the wwPDB's Remedation Project
Remediation of the Protein Data Bank archive has been published in Nucleic Acids Research's 2008 Database Issue.
K. Henrick; Z. Feng; W. F. Bluhm; D. Dimitropoulos; J. F. Doreleijers; S. Dutta; J. L. Flippen-Anderson; J. Ionides; C. Kamada; E. Krissinel; C. L. Lawson; J. L. Markley; H. Nakamura; R. Newman; Y. Shimizu; J. Swaminathan; S. Velankar; J. Ory; E. L. Ulrich; W. Vranken; J. Westbrook; R. Yamashita; H. Yang; J. Young; M. Yousufuddin; H. M. Berman Nucleic Acids Research (2008) 36: D426-D433. doi: 10.1093/nar/gkm937
All data in the PDB archive reflects the features incorporated as part of this wwPDB project, including standardized IUPAC nomenclature for chemical components, updated sequence database references and taxonomies, improved representations of viruses, and more.
These data are available through the FTP archive and wwPDB member sites.
Documentation about the Remediation Project is available at www.wwpdb.org.
Time-stamped Copies of PDB Archive Available via FTP
A time-stamped snapshot of the PDB archive (ftp.wwpdb.org) as of January 7, 2008 has been added to ftp://snapshots.rcsb.org/.
Snapshots of the PDB have been archived annually since 2004. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.
The script at ftp://snapshots.rcsb.org/rsyncSnapshots.sh may be used to make a local copy of a snapshot or sections of the snapshot.
The directory 20080107 includes the 48,161 experimentally-determined coordinate files that were current as of January 7, 2008. 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.
15-January-2008
Announcement: Data Processing Versioning Procedures
Data in the PDB archive currently follow either PDB File Format Version 3.0 or 3.1. This is indicated in REMARK 4 of the file.
Version 3.0 is the format used for files released as a result of the Remediation Project.
Since August 1, 2007, all files processed and released into the archive follow Version 3.1. When modifications are made to files released prior to that date, they are then re-released in Version 3.1.
Version 3.1 differs in descriptions of the biological unit (REMARK 300/350), geometry (REMARK 500), atom/residues modeled as zero occupancy (REMARK 475/480), non-polymer residues with missing atoms (REMARK 610), and metal coordination (REMARK 620). Documentation describing the differences between these versions is available at http://www.wwpdb.org/docs.html.
Beginning March 4, 2008, it will be indicated in the REVDAT record with the name "VERSN" when a Version 3.0 file is re-released as Version 3.1.
For example, if the journal record is updated in an entry that still follows Version 3.0, the REVDAT would appear as:
REVDAT 1 04-MAR-08 1ABC 1 JRNL VERSN
REVDAT 1 13-FEB-07 1ABC 0
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.
Documentation about file formats and the Remediation Project is available at www.wwpdb.org.
Positions Available
Available Positions with the RCSB PDB include openings at the University of California, San Diego for a Senior Scientist/Scientific Software Developer and for a Lead Web Architect.
08-January-2008
sf-convert: A Format Conversion Tool for Structure Factor Files
The command-line program sf-convert can easily translate data in various formats to the mmCIF format for use with ADIT validation and deposition software. sf_convert can also translate structure factors already released in the PDB from mmCIF to different formats.
This tool can input files from the following programs and formats:
mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, SHELX, SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, MULTAN, MAIN, and OTHER (an ASCII file with H, K, L, F, and SigmaF separated by a space).
sf-convert can then output the data formatted as mmCIF, MTZ, CNS, TNT, SHELX, EPMR, XTALVIEW, HKL2000, Dtrek, XSCALE, MULTAN, MAIN, or OTHER.
Beginning February 1, 2008, structure factor files will be required when depositing crystal structures to the PDB.
sf-convert is available for download from sw-tools.rcsb.org.
01-January-2008
2007 Annual Report Now Available
The RCSB PDB's 2007 Annual Report is currently being distributed. This snapshot provides an introduction to the resource and to recent accomplishments in data deposition, data access, and education. The 2007 report also describes the highlights of the wwPDB's Remediation Project.
The report is available as a PDF. If you would like a printed copy of the report, please send mail to [email protected].
2008 Calendar Now Available
A calendar showcasing PDB structures is now available online. Printed copies are also available via [email protected].
