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Year 2011 News

Contents:

27-Dec-2011 Happy Holidays
20-Dec-2011 Notice for REFMAC Users
13-Dec-2011 Looking for Ligands
13-Dec-2011 Paper Published
06-Dec-2011 Latest Website Release
29-Nov-2011 Search the PDB for homo- and hetero-multimer structures
22-Nov-2011 Customize Your RCSB PDB Homepage
15-Nov-2011 Molecule of the Month News
08-Nov-2011 Use the Top Bar Suggestion Box for Quick and Precise Searching
01-Nov-2011 New Target Registration Database
25-Oct-2011 PDB40 Symposium
18-Oct-2011 Newsletter published
11-Oct-2011 Educational Resources for Mobile Devices
04-Oct-2011 PDB Pioneers
27-Sep-2011 Poster Prize Awarded at IUCr
20-Sep-2011 New Structures Widget
13-Sep-2011 Latest Website Release
06-Sep-2011 Tools for Education
30-Aug-2011 Validate Structure Factor Diffraction Data with SF-Tool
23-Aug-2011 New pdb_extract Release
16-Aug-2011 wwPDB Events at IUCr (August 22-30, 2011)
16-Aug-2011 RCSB PDB Poster Prize at IUCr
09-Aug-2011 Poster Prize Awarded at ISMB
02-Aug-2011 Different Ways To Explore New Entries
02-Aug-2011 PDB40 Abstracts Due August 15
26-Jul-2011 Analyze small molecule interactions in the PDB with Ligand Explorer
26-Jul-2011 Travel Award Applications for PDB40 due August 1
19-Jul-2011 Travel Award Applications for PDB40 due August 1
19-Jul-2011 Protein Society Meeting
12-Jul-2011 ISMB and 3DSIG Meetings
05-Jul-2011 Newsletter published
28-Jun-2011 Browse Membrane Transport Proteins
21-Jun-2011 Build complex queries with Advanced Search
14-Jun-2011 Poster Prize Awarded at ACA
07-Jun-2011 Browse the PDB by GO Terms, EC Number, Source Organism, and More
31-May-2011 Enhanced Sequence Display
24-May-2011 Upcoming Meeting: ACA
17-May-2011 Validate Entries Before Deposition
10-May-2011 Educational Resources to Explore a Structural View of Biology
03-May-2011 Newsletter published
26-Apr-2011 Rutgers Day (April 30)
26-Apr-2011 New Publication
19-Apr-2011 Latest Website Release
12-Apr-2011 Narrated RCSB PDB Tutorial Updated
12-Apr-2011 DNA Day 2011: April 15
05-Apr-2011 J.P. Stevens HS Wins NJ Protein Modeling Event
29-Mar-2011 The Structural Biology of HIV
22-Mar-2011 Quick Jmol Views
15-Mar-2011 Visit us at the San Diego Science Festival on March 26
15-Mar-2011 Paper Published
08-Mar-2011 Depositing Structures with Ligands
01-Mar-2011 Upcoming Meetings
22-Feb-2011 Structural Neighbors
15-Feb-2011 Upcoming Meeting: AAAS Meeting and Family Days
08-Feb-2011 Create High Resolution Images
01-Feb-2011 Store Personal Annotations With MyPDB
25-Jan-2011 NJ Science Olympiad Protein Modeling Results
18-Jan-2011 Newsletter published
11-Jan-2011 Papers Published
04-Jan-2011 Structural Biology Knowledgebase Widget

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


27-Dec-2011

Happy Holidays


For some RCSB PDB highlights from the past year, be sure to download the 2011 Annual Report (PDF).

The PSI Structural Biology Knowledgebase has also created a 2012 Calendar (PDF).

20-Dec-2011

Notice for REFMAC Users

Depositors using REFMAC with TLS should make sure that the ATOM records contain full (and not residual) B factors before depositing an entry to the wwPDB.

When TLS is involved in refinement using a script, the keyword "tlsout addu" should be added to produce a coordinate file containing the full B factor. The latest REFMAC interface (in CCP4i) has a button "Add TLS contribution to XYZOUT" in the folder of TLS Parameters for adding this keyword.

If depositors have finished the final round of refinement without including "tlsout addu" keywords, and do not see ANISOU records in the coordinates, only the residual B factors have been generated in the coordinate file. The residual B factor needs to be updated to the full B factor in order to properly run validation checks.  

If needed, the TLSANL page at http://deposit.rcsb.org/adit/REFMAC.html provides web form server and scripting information for converting files.

13-Dec-2011

Looking for Ligands

All residues and small molecule components found in PDB entries, including standard and modified amino acids/nucleotides, small molecule ligands, ions, and solvent molecules, are described in the wwPDB's Chemical Component Dictionary.

The information stored in this dictionary can be easily searched using any of these query options:

  • Simple top bar searching (with autocomplete suggestions)
    Click on the Ligand icon (located above the top search box) to limit your search. Enter a ligand name or the 3-character chemical component ID. (More on top bar searching).

  • Chemical Component Search
    Chemical Component Search.

    This powerful form can be accessed by selecting the top bar ligand icon and then [ additional ligand options ]. Launch the chemical structure editor to draw a structure, or paste in a SMILES or SMARTS string, and then perform a substructure, exact, similarity, or superstructure search. In addition, ligands can be searched by name, identifier, formula, and molecular weight. A tutorial and screencast demonstrating the chemical structure search is available.


  • Advanced Search
    Advanced Search.

    Supports the searches mentioned above, plus additional searches by chemical component type, binding affinity, sub-component, and more. These types of searches can be combined and even amended with searches for the associated structures. Learn more about the advanced search with this tutorial with this list of available queries.

These searches will return a Ligand Summary page that contains an overview of the chemical component, 2D and 3D images, links to other resources, and links to related ligands and PDB entries. 

13-Dec-2011

Paper Published

The December issue of Nature Structural & Molecular Biology contains a special Essay Collection called Celebrating structural Biology (paywall). Coinciding with the 40th anniversary of the PDB, it features personal accounts that describe the history and predict the future of structural biology. Included are the reflections of RCSB PDB director Helen Berman on The evolution of the Protein Data Bank.

Tom L Blundell, Stephen C Harrison, Robert M Stroud, Shigeyuki Yokoyama, Lewis E Kay, Michael G Rossmann, Helen M Berman, Alexander Wlodawer, Elena Conti, Brian Kobilka, Janet M Thornton, David Cowburn, Nenad Ban, Olga Boudker (2011) Celebrating structural biology Nature Structural & Molecular Biology 18: 1304-1316 doi: 10.1038/nsmb1211-1304.

06-Dec-2011

Latest Website Release

Surface of PBCV-1 virus capsid with 5040 chains; one of the largest assemblies in the PDB (1m4x).
(Click image to enlarge)
Surface of PBCV-1 virus capsid with 5040 chains; one of the largest assemblies in the PDB (1m4x).

New and enhanced features have been added to the RCSB PDB website, including:

* Visualizing Molecular Surfaces. Protein Workshop now supports molecular surfaces to aid in the display of quaternary structure, protein-protein interactions, and binding sites. A detailed description of how to use this feature is available. The program is one of the molecular viewing options available from every Structure Summary page.

* Exploring ligands. Improved Jmol visualization, information about subcomponents, and links to DrugBank are some of the features added to Ligand Summary pages. Additionally, binding affinity data from PDBbind have been added to the External Ligand Annotations widget on Structure Summary pages.

* Access pre-released sequences via Web Services. The RCSB PDB supports RESTful Web Services can be used to help software developers access data more easily.  A new service for accessing pre-released sequences in FASTA format has been added; information about all possible services is available.

The What's New page has complete descriptions of all the new features.

29-Nov-2011

Search the PDB for homo- and hetero-multimer structures

PDB entry 3Q5F.
PDB entry 3Q5F.

The following Advanced Search options (listed under Structure Features) can be combined to find homo- and hetero-multimer structures in the PDB:

  • Number of Chains (Biological Assembly): specifies the number of polymeric chains in a multimer
  • Number of Entities: limits the number of unique polymeric units (protein, DNA, or RNA) in a multimer
  • Structure Features/Macromolecule Type: selects the type(s) of macromolecule to be included in the multimer (protein, DNA, RNA, and/or DNA/RNA hybrid).

Different examples are shown below, with the query constraints selected. Click on the image to enlarge.

Example 1: Find all homodimers and heterodimers that only contain protein. The results set will include entries that contain exactly two protein chains. The search entries that contain only one or more than two protein chains, and excludes nucleic acids.

Example 2: Find entries containing only protein heterodimers. The results set will include entries that contain two different protein chains. Entries containing homo-multimers, nucleic acid chains, or more than two protein chains will be excluded.

Example 3: Find entries containing only protein homotetramers. The results set will include entries that contain exactly four identical protein chains. Entries containing heterotetramers, nucleic acid chains, or any number of chains other than four will be excluded.

Example 4: Find protein homodimers bound to DNA. The results set will include entries that contain DNA (mostly duplexes) bound to two copies of the same protein chain (a dimer).

Additional information about Advanced Search is available.

22-Nov-2011

Customize Your RCSB PDB Homepage

Customize the RCSB PDB homepage with different widgets.
(Click image to enlarge)
Customize the RCSB PDB homepage with different widgets.

The RCSB PDB homepage is comprised of web widgets that can be moved around, minimized, or hidden so users can create a website that reflects their interests. Frequently-used features can be moved to the top, while less popular items can be hidden or collapsed.

All widgets with a dark blue bar on top can be moved around on the page by dragging the arrow buttons. The options shown in the widget can be collapsed by selecting "Hide".

Select the Customize This Page button from the left menu to choose which sections are displayed.

Options in the default view include:

Featured Molecules

Read the latest descriptions of the RCSB PDB's Molecule of the Month and the PSI SBKB's Featured System.

Latest Structures
Scrolls through a slideshow of individual entries that displays the entry title, image, citation, and a link to the PubMed abstract, if available. Pause the show at any point to read the entire abstract, click to view the entry's Structure Summary page, or go straight to the Jmol view of the entry.

Explore Archive
Tour the PDB archive by "drilling-down" on significant properties of structures like "Organism" and "Polymer type", with just a few clicks. The widget also gives a quick statistical overview of the PDB. Users can browse the charts individually, or view them all together by clicking on the "Show all" link.

New Structures
Links to the latest release, structure papers included in a release, and to the Unreleased Entry Search.

New Features
Scrolls through the latest website features and improvements with links to detailed descriptions.

RCSB PDB News
Read the latest updates and highlights, with links to the Quarterly Newsletter and other publications.

wwPDB News
Updates from wwPDB.org are linked in this widget.

FTP Archives
Links to the current FTP archive and to archival snapshots.

Widgets not included in the default view that can be added are:

Download Files
Provides a form on the home page to easily download any number of structures in a variety of formats.

Structure Comparison

Run pairwise structural and sequence alignments.

Sequence Search
Enter a PDB ID or sequence to query for similar sequences.

ADIT Deposition
Provides a quick interface to the RCSB PDB ADIT deposition services. Users can start a new deposition, or continue an existing session.

Select a combination of widgets to display, and then move the widgets around to customize the display.
Structure Summary pages and query result pages can be similarly customized.

15-Nov-2011

Molecule of the Month News

Subscribe to the new RSS feed
(Click image to enlarge)
Subscribe to the new RSS feed.

The RCSB PDB's Molecule of the Month and related resources help promote a structural view of biology.  Visit the latest Molecule of the Month-related features at PDB-101, including:

  • RSS Feed. Subscribe to the PDB-101 RSS (Really Simple Syndication) Feed to access Molecule of the Month columns as they are published. This feed pushes the articles to RSS readers so users can easily view the latest articles. Access this feed by selecting the RSS icon PDB-101 header.

  • Toll-like Receptors (TLRs). November's Molecule of the Month feature explores TLRs and the innate immune system in honor of the 2011 Nobel Prize in Physiology or Medicine. The award was divided, one half jointly to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity and the other half to Ralph M. Steinman for his discovery of the dendritic cell and its role in adaptive immunity.

In his research, Beutler and colleagues discovered the role of a TLR that recognizes lipopolysaccharide. A downloadable flyer (PDF) highlights an example of this TLR structure using PDB IDs 3fxi and 2j67.  

For a complete look at recent additions to Molecule of the Month and PDB-101, see the What's New page.

08-Nov-2011

Use the Top Bar Suggestion Box for Quick and Precise Searching

blank image.
(Click image to enlarge)
Top Bar Suggestion Box.

The top search bar has been redesigned to help users easily and intuitively create precise searches.

Typing in the top search bar displays an interactive pop-up box with suggestions of common PDB search terms, organized in different categories. This autocomplete feature makes suggestions based on even a few letters.

These categories return more precise results than simple text searches. For example, entering the word human presents several options organized by category (such as Molecule Name, Author, Organism). Suggestions include the number of results and link to the set of matching structures. Results for Organism Homo sapiens (human) will not include entries of author Human, J.

The redesigned top search can be also be limited to quick searches on Author, Macromolecule name, Sequence, or Ligand by selecting the related icon.

The order of results of a PDB text search or a sequence search is now based on the relevance of the term (for a text search) or the alignment score (for a sequence search). Search results can be further refined using Advanced Search or by drilling down through the pie charts organized by major categories.

01-Nov-2011

New Target Registration Database

TargetTrack.
TargetTrack.

A new experimental data tracking database, TargetTrack (sbkb.org/tt), shows the latest information on the progress of structural studies on registered protein targets.  This information provided by worldwide structure genomics centers can help many biological researchers with their project's experimental design.

TargetTrack is a combination of existing structural target databases, TargetDB and PepcDB, and includes additional information about protein complexes, membrane proteins, cryoEM studies, and other advances in structural biology. At this time, both databases are operating in parallel, but TargetTrack will replace the existing databases in January 2012. If you are a user of TargetDB-PepcDB with questions, please contact target-help@sbkb.org.

25-Oct-2011

PDB40 Symposium

PDB40 Symposium logo.

Celebrate four decades of innovation in structural biology this weekend with the wwPDB. A special Cold Spring Harbor Laboratory symposium will honor the PDB's 40th anniversary and the many scientific contributions it archives. Limited space is available--register today!

PDB40 will begin at 5:30 p.m. with an evening reception, dinner, and oral session on Friday, October 28th and conclude after lunch on Sunday, October 30, 2011. The preliminary program is available online (PDF), and will be distributed at the meeting.

During the meeting, from the opening reception and continuing through the closing lunch, 93 posters will be displayed. The online-only poster abstract book is available as a PDF. Presenters should stand by their posters during the dedicated sessions (Friday evening and Saturday from 5:00 p.m. - 6:30 p.m).

Attendees can also participate in activities relating to the PDB's past and future. To provide a historical perspective, Cold Spring Harbor Laboratory has organized a display of pictures from the 1971 meeting. Some of the people shown in the photos have been identified, but many have not. Space will be provided to write down the names of the people to help update the CSHL archives.

To help the wwPDB look towards the future, we're asking participants to imagine what the PDB will be like 10 and 40 years from now.  Throughout the meeting, attendees can write down their predictions and post them to our board.

The wwPDB organizers of this event are grateful to our industrial sponsors and funding agencies listed at the PDB40 website for their support of this meeting.

18-Oct-2011

Newsletter published

The fall 2011 issue (HTML | PDF) highlights updates of pdb_extract and the SF-Tool, the latest website release, new additions to PDB-101, and the latest on the PDB40 symposium.

In this issue's Education Corner, Christopher Smith gives his Insights into Molecular Modeling for the Middle Schooler.

The newsletter also describes the many ways users can explore new entries, the RCSB PDB poster prize awardees, recent website and deposition statistics, and more.  

This quarterly newsletter is published  online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

11-Oct-2011

Educational Resources for Mobile Devices

Molecule of the Month ePubs.

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Molecule of the Month ePubs.

PDB-101, the educational view of the RCSB PDB, has enabled special features for mobile devices. 

  • Molecule of the Month ePubs: Every Molecule of the Month article is now available as an downloadable ePub document.  ePubs can be viewed offline in ePub readers on mobile devices (such as iBooks for Apple mobile devices, and Aldiko for Android devices).

To download a Molecule of the Month ePub, click on the link at the top of any feature.
ePub (Electronic Publication) is an open standard for digitally published documents.

  • Interactive Molecular Views: PDB-101 Structure Focus pages, which highlight the PDB entries highlighted in Molecule of the Month articles, feature interactive molecular views.
Users on mobile devices can rotate the molecule about the Y-axis by dragging on the image left and right. For an example, see the Structure Focus on ribonuclease A entry 5rsa.

For more intensive mobile usage, the PDBMobile webapp for Apple mobile devices can be used to quickly access basic structure and citation information from the RCSB PDB servers. PDBMobile users are encouraged to take a brief survey about their experiences with the application.

04-Oct-2011

PDB Pioneers

PDB Pioneers.
(Click image to enlarge)
PDB Pioneers.

In honor of the upcoming PDB40 symposium, October's Molecule of the Month looks at the structures available in the archive's early days: myoglobin, hemoglobin, lysozyme, carboxypeptidase, subtilisin, chymotrypsin, papain, pancreatic trypsin inhibitor, lactate dehydrogenase, rubredoxin, and cytochrome b5.

The PDB40 symposium will celebrate four decades of innovation in structural biology this fall at a Cold Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the many scientific contributions it archives.

PDB40 will begin with an early evening reception, dinner, and oral session on Friday, October 28th and conclude with lunch on Sunday, October 30, 2011. Information about the meeting is available online at meetings.cshl.edu/meetings/pdb40.shtml.
Limited space at PDB40 is available--register today!

27-Sep-2011

Poster Prize Awarded at IUCr

Serah Kimani
(Click image to enlarge)
Serah Kimani
Adriana Kantchevae
(Click image to enlarge)
Adriana Kantcheva

The RCSB PDB Poster Prize at the XXII Congress and General Assembly of the International Union of Crystallography (IUCr, August 22-30, Madrid, Spain) went to Serah Kimani for Unexpected reactions resulting from mutating catalytic residues in an amidase reveal the role of the catalytic unit (Serah Kimani,a Trevor Sewell,b aDepartment of Molecular and Cell Biology, University of Cape Town, Cape Town (South Africa). bElectron Microscope Unit, University of Cape Town, Cape Town (South Africa)).

Serah will receive an Early Career Scientist Travel Award to attend the PDB40 symposium to be held at Cold Spring Harbor Laboratory, October 28-30.

The judging committee also recognized Adriana Kantcheva with an honorable mention for Structure of the chloride dependent E290S-LeuT mutant from Aquifex aeolicus (Adriana K. Kantcheva,a Anne-Marie Lund Winther,a Matthias Quick,b Jonathan A. Javitch,b and Poul Nissen,a aCenter for Structural Biology, Dept. Molecular Biology, University of Aarhus (Denmark). bCenter for Molecular Recognition, Dept. Pharmacology, Columbia University, New York).

Adriana will receive a subscription to Science.

Many thanks to the judges, who worked through all six days of poster presentations: Bernhard Rupp (k.k.Hofkristallamt), Kam Zhang (RIKEN), Manfred Weiss (Helmholtz-Zentrum Berlin), Jochen Mueller Dieckmann (EMBL-Hamburg), George Phillips (University Wisconsin-Madison), Clyde Smith (Stanford Synchrotron Radiation Laboratory), Miroslav Cygler (National Research Council Canada).

Special thanks to the Poster Judging Committee Chair Katherine Kantardjieff (California State University San Marcos) and to the IUCr.

20-Sep-2011

New Structures Widget

Quickly find new entries, related structure articles, and unreleased articles in the "New Structures" widget, located on the top right section of the home page.

This widget provides easy access to:

 
Check out the What's New page for complete descriptions of the newest RCSB PDB website features.

13-Sep-2011

Latest Website Release

A new home page widget to explore the PDB archive.
(Click image to enlarge)
A new home page widget to explore the PDB archive.

New and enhanced features have been added to www.pdb.org, including:

  • Top search bar: The redesigned top search bar helps users easily and intuitively create both broad and precise searches. Start typing in the box provided to access a suggestion box of related terms and links to searches.  This box can be used to search a variety of categories, or limited to citation author, macromolecule name, sequence, or ligand.

The order of results of a PDB text search or a sequence search are now based on the relevance of the term (for a text search) or the alignment score (for a sequence search).

  • Explore Archive Widget: Tour the PDB archive by "drilling-down" on significant properties of structures like "Organism" and "Polymer type", with just a few clicks using the home page's new Explore Archive widget. The "Explore Archive" widget also gives a quick statistical overview of the PDB. Users browse can browse the charts individually, or view them all together by clicking on the "Show all" link.

This widget applies the same drill down options available from each set of search results to the contents of the entire archive.

  • PDB-101 Structure Focus: Learn about the individual entries discussed in Molecule of the Month articles. Each Structure Focus page provides a description that explains why it was selected as an example structure, and offers an interactive 3D representation of the structure, sequence display, ligand information, and links to any other articles discussed in the Molecule of the Month feature. As an example, see the Structure Focus on hemoglobin entry 2hhb.

PDB-101 is a unique view of the RCSB PDB that packages together the resources of interest to teachers, students, and the general public.

  • Search for structures by protein modification. The Protein Modification Browser was constructed based on protein modification ontology (PSI-MOD) from the Proteomics Standards Initiative (http://www.psidev.info/). From here users can browse protein residue modifications, view the number of associated PDB entries, and search for associated structures.

The Protein Modification options in Advanced Search have been expanded to include the protein modification source type (Name, Keyword, RESID, PSI-MOD, and Chemical Component Dictionary) and the associated name/ID of the modification.

The What's New page has complete descriptions of all the new features.

06-Sep-2011

Tools for Education

Click on the blackboard logo from the top of any page to enter PDB-101.
(Click image to enlarge)
Click on the blackboard logo from the top of any page to enter PDB-101.

PDB-101 packages together resources that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.  Major topics include:

  • Structural View of Biology. Built around the Molecule of the Month series, this feature promotes a top-down exploration of the PDB. Starting with high-level functional categories, readers can browse through descriptive subcategories to access relevant articles that describe molecules in simple terms and access the related PDB entries. Mouseovers, pulldown menus, and carousels all offer easy navigational tools to promote learning.
  • Molecule of the Month. Since 2000, the RCSB PDB has published articles that describe the structure and function of a molecule along with interactive views, discussion topics, and links to structure examples. The collection of these articles provides a annotated view of the PDB archive. Molecules of the Month columns appear on single pages, with links to printable PDF versions and downloadable high resolution images. They can be accessed using the pulldown menu in the top bar, through the Structural View of Biology interface, and by archives organized by title, date, and category.
  • Related Educational Resources and materials, including posters, animations, and classroom lessons and activities.  Recently, a poster (PDF) and animation of the structure of the HIV virus was added.
  • Understanding PDB Data, a reference to help explore and interpret individual PDB entries. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges to exploring the archive.

To enter PDB-101, click on the blackboard PDB-101 logo or its related widget in the left-hand menu reveals an education-centered website. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the upper-left PDB-101 pulldown menu to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to access RCSB PDB deposition and query services from the main website.

Related materials for learning about the RCSB PDB website include a suite of tools (narrated tutorial, slides, and exercises) from openhelix.com; short online screencasts that demonstrate how to use different RCSB PDB tools; and contextual help and examples available where a   appears.

30-Aug-2011

Validate Structure Factor Diffraction Data with SF-Tool

SF-Tool is a streamlined, web-based tool for validating structure factor diffraction data files.  The latest release includes support for neutron and hybrid experiments; incorporates checks from REFMAC1, PHENIX2, and SFCHECK3; and converts multiple data sets into a single mmCIF file.

Visit sf-tool.rcsb.org to:

  • Validate model coordinates against structure factor data for X-ray and neutron data
  • Easily convert structure factor files between different formats (mmCIF, MTZ, CNS/CNX, XPLOR, SHELX, TNT, HKL2000, SCALEPACK, D*Trek, SAINT, and more)
  • Check for and validate twinned or detwinned data

Documentation for this program is available. Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.

1Refinement of Macromolecular Structures by the Maximum-Likelihood Method. G.N. Murshudov, A.A. Vaguine, E.J.Dodson (1997) Acta Cryst. D53: 240-255.

2PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. H. Zwart (2010) Acta Cryst. D66: 213-221

3SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. A.A. Vaguine, J. Richelle, S.J. Wodak (1999) Acta Cryst. D55: 191-205.

23-Aug-2011

New pdb_extract Release

pdb_extract
pdb_extract.

Version V3.11 of pdb_extract has been released as an online web tool and a downloadable workstation program.

pdb_extract is a program that minimizes errors and saves time during the deposition process by extracting key details from the output files produced by many X-ray crystallographic and NMR applications. The program merges these data into macromolecular Crystallographic Information File (mmCIF) data files that can be used with ADIT for validation and deposition.

New features include:

  • Data from hybrid method experiments
  • NCS and TLS ranges in BUSTER and REFMAC
  • Improved mtz to mmCIF conversion
  • Quality assessment of X-ray data

Complete details are available in the release notes and manual.

Depositors can upload files into the pdb_extract webserver or download the latest workstation version at pdb-extract.rcsb.org. Tutorials are also available for X-ray and NMR.

16-Aug-2011

wwPDB Events at IUCr (August 22-30, 2011)

IUCr meeting.
(Click image to enlarge)
IUCr meeting

Meet wwPDB directors and staff from around the globe at the XXII General Assembly and Congress of the International Union of Crystallography (IUCr, August 22-30, 2011) in Madrid, Spain.

Download this PDF to see the events listed below in calendar form:

wwPDB Q&A Session (Thu Aug 25, 1:40 - 2:40pm). Come to Room Paris for an open discussion with the wwPDB directors about issues important to you and the PDB.

Oral Presentations

RCSB PDB Director Helen M. Berman will discuss The wwPDB and future perspectives in sharing macromolecular structure data as part of the session Developments and directions for crystallographic databases (MS27 Wed Aug 24, 3-5:35pm), chaired by RCSB PDB's Senior Software Architect John Westbrook and Saulius Gražulis (Vilnius University) in Room Londres.

In Friday's Keynote Lecture 16, Gerard Kleywegt (Head of PDBe) will address Validation and errors in protein structures (Fri Aug 26, 9-9:50am) in Auditorium A.

Later that morning, Swanand Gore (scientific programmer, PDBe) and Marina Zhuravleva (annotator, RCSB PDB) will describe Validation of small molecule and macromolecular X-ray structures. What are the differences and how can we learn from each other? together with Matthew Lightfoot (CCDC) as part of the session on Validation, error detection, and fraud prevention (MS43 Fri 43, Aug 26, 10:15am-12:15pm) in Auditorium A.

John Westbrook will present The wwPDB Working Format: A simplified application of CIF technology on Monday as part of the COMCIFS session (MS89 Archiving, exchange and retrieval of scientific data in the 21st century, Mon Aug 29, 10:15-12:50) in Room Londres.

Poster Presentations

Learn about The wwPDB Common Tool for Deposition and Annotation as presented by RCSB PDB Deputy Director Martha Quesada on Tue Aug 23 and Wed Aug 24 (MS27.P02(C403)).

During the poster session on Sat Aug 27 and Sun Aug 28, PDBj's Akira Kinjo will describe the Protein Data Bank on the semantic web (MS89.P01(C760)).

Exhibit Booth #51

Visit the wwPDB exhibit booth for demonstrations, conversations, materials, and more.

16-Aug-2011

RCSB PDB Poster Prize at IUCr

The RCSB PDB Poster prize will be awarded to the best student poster involving macromolecular crystallography at the IUCr meeting.

Authors who intend to be nominated to the awards should collect an identification color label from the reception desk at the meeting, not later than 18.30 h of the day before to the scheduled poster session. These labels should be attached onto the top right hand corner of their posters.

Prizes will be announced during the closing ceremony and later on this website.

Past RCSB PDB awards are posted online.

09-Aug-2011

Poster Prize Awarded at ISMB

RCSB PDB poster prize winner Tammy Cheng.
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RCSB PDB poster prize winner Tammy Cheng.

The RCSB PDB Poster Prize at the 19th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB, July 15-19; Vienna, Austria), went to Tammy Cheng for Structural biology meets systems biology: Gauging the systemic impact of non-synonymous single nucleotide polymorphisms (Tammy M. K. Cheng1, Linda Jeffery2, Lucas Goehring3, Yu-En Lu4, Jacqueline Hayles2, Bela Novak5, Paul A. Bates1

1Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute; 2Cell Cycle Laboratory, Cancer Research UK London Research Institute; 3Max Plank Institute for Dynamics and Self-Organization, Göttingen, Germany; 4Computer Laboratory, University of Cambridge, UK; 5Department of Biochemistry, University of Oxford, UK

Tammy will receive a subscription to Science and a copy of Structural Bioinformatics (Gu, Bourne, editors).

Many thanks to the judges: Emidio Capriotti (Stanford), Jeroen de Ridder (Delft University of Technology), Javier Diaz (University of Toronto), Nils Gehlenborg (Harvard Medicial School), Milana Frenkel-Morgenstern (Weizmann Institute), Arik Harel (Rutgers), Edda Kloppmann (Technische Universität München), Nathan Nehrt (University of Maryland, Baltimore County), Venkata P. Satagopam (EMBL Heidelberg), Christian Schäfer, Andrea Schafferhans, Markus Schmidberger (Technische Universität München). Thanks also to Poster Committee Chair Yana Bromberg (Rutgers University) and to the International Society for Computational Biology.

An RCSB PDB poster prize will also be awarded at the upcoming IUCr meeting.

02-Aug-2011

Different Ways To Explore New Entries

The Latest Structures widget, located on the home page, cycles through newly released entries.
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The Latest Structures widget, located on the home page, cycles through newly released entries.

On average, the wwPDB releases 170 structures into the PDB archive each week. The RCSB PDB offers different ways of exploring these new entries:

  • The Latest Structures widget on the home page provides a slideshow of individual entries. It displays the entry title, image, citation, and a link to the PubMed abstract, if available. Users can pause the show at any point to read the entire abstract, click on the entry title to view the entry's Structure Summary page, or go straight to the Jmol view of the entry.
  • The set of recently released structures can be launched in the Query Results Browser by clicking on the date listed at the top of the page, the link provided in the Latest Structures widget, and the link to the Latest Release from the left hand Search menu. From the Query Result Browser, users can drill through by category (organism, taxonomy, experimental method, and more), generate reports, and download structure and sequences files.
  • The MyPDB service can be set to run saved searches with each update. Email alerts (weekly or monthly) will be sent when new entries matching the search are released in the PDB archive.

02-Aug-2011

PDB40 Abstracts Due August 15

Celebrate four decades of innovation in structural biology this fall at a Cold Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the many scientific contributions it archives.

The meeting will also host a session of poster presentations. To submit your abstract for consideration, please submit online following the link provided after registration. The status of abstracts will be posted as soon as decisions have been made by the organizers. The deadline for poster submission is August 15, 2011.

PDB40, organized by the Worldwide Protein Data Bank (wwPDB), will begin with an evening reception, dinner, and oral session on Friday, October 28th and conclude with lunch on Sunday, October 30, 2011.

Early registration is strongly encouraged as the meeting is expected to fill quickly. For complete meeting details, see http://meetings.cshl.edu/meetings/pdb40.shtml.

26-Jul-2011

Analyze small molecule interactions in the PDB with Ligand Explorer

Ligand Explorer can be used to dynamically display the interactions in PDB entry 2w70
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Ligand Explorer can be used to dynamically display the interactions in PDB entry 2w70.

Ligand Explorer (PDF Flyer) displays hydrogen bonds, hydrophobic interactions, bridged H-bonds, metal interactions, and neighbor residue interactions and thresholds in a dynamic viewer.

Toggle interactions on/off, adjust distance thresholds, label interactions by distance, and display all neighbor residues. Distances, angles, and dihedral angles can be analyzed and measured.  The views created can be saved as a text file listing interactions or as an image file (instructions available for creating high resolution images).

Ligand Explorer can be accessed from the Ligand Chemical Component section of an entry's Structure Summary page. The program uses the same Molecular Biology Toolkit1 as the RCSB PDB's Protein Workshop and Simple Viewer.

Launching Ligand Explorer can install a local copy of the program on your computer, and can be used to read a local PDB file, or access a PDB file directly using the File menu (when online).

1The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications
(2005) BMC Bioinformatics, 6: 21.

26-Jul-2011

Travel Award Applications for PDB40 due August 1

Limited funds are available to help students and early career scientists attend PDB40 (October 28 - 30, 2011 at Cold Spring Harbor Laboratory). Preference will be given to those who have submitted poster abstracts. To apply for assistance, download the application form from the PDB40 website, and email info@wwpdb.org the completed form, a copy of your abstract, and a supporting letter from your research advisor/department chairman. Funds are non-transferable. Awards will be distributed after the meeting. Applications are due by August 1, 2011.

19-Jul-2011

Travel Award Applications for PDB40 due August 1

blank image.

Limited funds are available to help students and early career scientists attend PDB40 (October 28 - 30, 2011 at Cold Spring Harbor Laboratory). Preference will be given to those who have submitted poster abstracts. To apply for assistance, download the application form from the PDB40 website, and email info@wwpdb.org the completed form, a copy of your abstract, and a supporting letter from your research advisor/department chairman. Funds are non-transferable. Awards will be distributed after the meeting. Applications are due by August 1, 2011.

19-Jul-2011

Protein Society Meeting

Protein Sociey logo.

At the 25th anniversary symposium of the Protein Society (July 23-27, 2011; Boston, MA), annotator Ezra Peisach will discuss The PDB at 40: Past, Present, and Future during the poster presentations.  Stop by poster B10 on Tuesday July 26 to learn more.

12-Jul-2011

ISMB and 3DSIG Meetings

At the 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (July 15-19; Vienna, Austria), Senior Scientist Andreas Prlić will describe A Census of Internal Pseudo-Symmetries and Similarities in Protein Domains at the Laptop/Poster session at 3Dsig satellite meeting. Scientific Lead Peter Rose will help users Become an Expert User of the RCSB Protein Data Bank Website and Web Services at the Technology Track session on Monday, July 18 at 2:30 p.m.

Also at ISMB, the RCSB PDB Poster Prize will be awarded for the best student poster presentation in the category of Structure and Function Prediction.

05-Jul-2011

Newsletter published

The summer 2011 newsletter (HTML | PDF) highlights PDB 40's program, poster session, and travel awards along with the latest developments in data deposition, data query, and outreach and education.

The Education Corner focuses on the American Association for the Advancement of Science's report Vision and Change in Undergraduate Biology Education: A Call to Action.

The newsletter also describes new options for generating Validation Reports, and highlights the Browse Database option of exploring the PDB archive using hierarchal trees organized by GO terms, EC number, source organism, and more.

The newsletter is published quarterly online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

28-Jun-2011

Browse Membrane Transport Proteins

Use the Transporter Classification Browser to find PDB's membrane transport proteins as organized by TC Database family (www.tcdb.org). The browser will autocomplete search terms with the matching classifications, and highlight locations on the tree.
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Use the Transporter Classification Browser to find PDB's membrane transport proteins as organized by TC Database family (www.tcdb.org). The browser will autocomplete search terms with the matching classifications, and highlight locations on the tree.

The Transporter Classification Database (www.tcdb.org) organizes membrane transport proteins using the Transporter Classification (TC) system. It is similar to the Enzyme Commission (EC) system, but incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. Transport systems are classified on the basis of five criteria, and each of these criteria corresponds to one of the five numbers or letters within the TC number for a particular type of transporter.

Select the Transporter Classification tab from the Browse Database interface to browse TC superfamilies, view the number of associated PDB structures, and explore individual structures.

Advanced Search can be used to combine searches for transporter classifications with queries for other specific types of data. Select the Transporter Classification Browser option from the Biology section of the Advanced Search pull-down menu.

21-Jun-2011

Build complex queries with Advanced Search

Advanced search provides the capability of combining multiple searches of specific types of data in a logical AND or OR. The result is a list of structures that comply with ALL or ANY of the search criteria, respectively.

Individual data items are organized by category; contextual help and examples are available by selecting . Recently added items include protein modifications, Pfam ID, and EM structures with experimental data. Currently, users can build searches based on:

  • ID(s) and Keywords: PDB, PubMed, UniProtKB, Pfam IDs; text searching
  • Structure Annotation: Structure title, description; and macromolecule name
  • Deposition: Author name; Deposit Date; Release Date; Latest Released Structures; Latest Modified Structures; Structural Genomics Project
  • Structure Features: Macromolecule Type; Number of Chains (asymmetric unit or biological assembly), entities; Models, and Disulfide Bonds; Molecular Weight; Secondary Structure Content; secondary structure length; SCOP, CATH, taxonomy
  • Sequence Features: sequence; translated nucleotide sequence; sequence motif; chain length; protein modifications; genome location
  • Chemical Components: name; ID; InChi descriptor; SMILES/SMARTS; molecular weight; chemical formula; binding affinity; has ligands; has modified residues
  • Biology: Source; expression organism; Enzyme Classification; biological process; cell component; molecular function; Transporter Classification
  • Methods: experimental method; X-ray resolution, R factor, diffraction source, reflections, cell dimensions, software, space group, crystal properties, detector; EM assembly
  • Publication: citation; MeSH terms; PubMed abstract
  • Misc: Has external links

The number of entries matching each individual query can be shown before running the full Advanced Search. Searches can also be filtered by removing sequence similarity.

Advanced Searches can be stored in MyPDB to be run or modified at any time.

14-Jun-2011

Poster Prize Awarded at ACA

Briony Yorke.
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Briony Yorke.

The RCSB PDB Poster Prize at the 2011 Meeting of the American Crystallographic Association (ACA, May 28-June 2; New Orleans, LA), went to Briony Yorke for New Approaches to Time-Resolved Structural Studies of Macromolecules. Briony Yorke1, Arwen Pearson1, Mike Webb1, Robin Owen.2
(1The University of Leeds, Leeds, United Kingdom, 2Diamond Light Source Ltd, Didcot, United Kingdom).

Briony will receive a subscription to Science and a copy of The International Tables of Crystallography Volume F.

Many thanks to the judges: Thomas Edwards (Emerald BioStructures), Katrina Forest (University of Wisconsin-Madison), and John Rose (The University of Georgia), and to Marcia Colquhoun and the ACA.

The prize will also be awarded at the upcoming ISMB and IUCr meetings.

07-Jun-2011

Browse the PDB by GO Terms, EC Number, Source Organism, and More

The RCSB PDB's Browse Database feature can be used to explore the PDB archive using different hierarchical trees. Browsers are available to search for related terms and structures based upon the following classifications:

The Browse Database feature can be accessed under the Search widget in the left-hand menu. Each tab links to a different browser.

31-May-2011

Enhanced Sequence Display

Protein modifications mapped onto the sequence diagram and Jmol view of PDB entry 1B0V.
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Protein modifications mapped onto the sequence diagram and Jmol view of PDB entry 1B0V.

The sequence tab available from each PDB entry's Structure Summary page was recently enhanced and improved.

The sequence tab offers a diagram representation of the sequence. Each macromolecule chain can be annotated with domain assignments, secondary structure, and structural features such as SNPs (Single Nucleotide Polymorphism), sites defined in the structure entry (i.e., binding sites of ligands) and protein modifications (i.e., posttranslational modifications). These annotations can be mapped on to the 3D Jmol view of the entry for further exploration.

Using the Display Parameters box, users can toggle between the display of unique chains and all chains. By default, only unique chains are displayed. This box can also toggle the display of the UniProtKB reference sequence.

For more information about the sequence tab and about other features recently added to the website, see the What's New page.

24-May-2011

Upcoming Meeting: ACA

Visit us for demonstrations, presentations, and posters.
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Visit us for demonstrations, presentations, and posters.

From May 28-June 2, the RCSB PDB will be at the 2011 Meeting of the American Crystallographic Association in New Orleans, LA.

  • Stop by exhibition booth 507 to meet with members of the RCSB PDB and the PSI Structural Biology Knowledgebase (PSI SBKB) and pick up many new materials. Learn about new features such as the Validation Server, PDB-101, the wwPDB Common Tool for Deposition and Annotation, and much more.
  • On Sunday, director Helen Berman will present "Putting the data in data mining: Curating the PDB archive" as part of the Use of Databases in Structural Biology session in room Borgne.
  • On Monday, learn about the PSI SBKB from Maggie Gabanyi during the session on the Protein Structure Initiative: Tools for the Home Lab.
  • A poster describing The wwPDB Common Annotation and Deposition Tool Development will be presented by Jasmine Young on Tuesday (T26).
  • The RCSB PDB Poster Prize will be awarded to recognize a student poster presentation involving macromolecular crystallography.

17-May-2011

Validate Entries Before Deposition

Depositors are encouraged to generate Validation Reports to monitor improvements made to structural models before deposition.

The RCSB PDB's Validation Server can be used to create validation reports outside of the deposition pipeline. Two options are available:

  • In the plain text report option, the server first checks the format consistency of the coordinates in the PRECHECK step. The precheck will produce a brief report identifying any changes that need to be made in your data files in order to obtain a validation report. In the validation step, the server produces an Atlas entry, a summary report, and a collection of structural diagnostics including bond distance and angle comparisons, torsion angle comparisons, base morphology comparisons (for nucleic acids), and molecular graphic images. Reports from PROCHECK1, NUCheck2, SFCheck3, and MolProbity4 are made available.
  • A new PDF report option produces a report that contains high-level geometric and experimental checking results without listing the detailed geometry. This unofficial report is similar to the wwPDB's PDF report generated during the annotation process for depositors to include with their journal submissions.

The Validation Server is available from the RCSB PDB Deposition Services page.

1 RA Laskowski, MW McArthur, DS Moss, JM Thornton (1993) J. Appl. Cryst. 265:283-291.
2 Z Feng, J Westbrook, HM Berman (1998) NUCheck. NDB-407 Rutgers University, New Brunswick, NJ.
3 AA Vaguine, J Richelle, SJ Wodak (1999) Acta Crystallogr. D55:191-205.
4 SC Lovell, IW Davis, BW Arendall, PIW de Bakker, JM Word, MG Prisant, JS Richardson, DC Richardson (2003) Protein Struct. Funct. Genet. 50:437-450.

10-May-2011

Educational Resources to Explore a Structural View of Biology

Click on the PDB-101 blackboard logo from the top of any page to access a new and unique view of the RCSB PDB.
(Click image to enlarge)
Click on the PDB-101 blackboard logo from the top of any page to access a new and unique view of the RCSB PDB.

PDB-101 packages together the resources of interest to teachers, students, and the general public--Structural View of Biology, Educational Resources, Molecule of the Month, and Understanding PDB Data--to promote exploration in the world of proteins and nucleic acids.

From any page, clicking on the blackboard PDB-101 logo or its related widget in the left-hand menu reveals an education-centered website. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the upper-left PDB-101 pulldown menu to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to access RCSB PDB deposition and query services from the main website.

This initial release of PDB-101 offers:

  • Structural View of Biology. Built around the Molecule of the Month series, this feature promotes a top-down exploration of the PDB. Starting with high-level functional categories, readers can browse through descriptive subcategories to access relevant articles that describe molecules in simple terms and access the related PDB entries. mouseovers, pulldown menus, and carousels all offer easy navigational tools to promote learning.
  • Molecule of the Month. Since 2000, the RCSB PDB has published articles that describe the structure and function of a molecule along with interactive views, discussion topics, and links to structure examples. The collection of these articles provides a annotated view of the PDB archive. With PDB-101, all Molecules of the Month columns appear on single pages, with links to printable PDF versions and downloadable high resolution images. They can be accessed using the pulldown menu in the top bar, through the Structural View of Biology interface, and by archives organized by title, date, and category.
  • Related Educational Resources and materials, including posters, animations, and classroom lessons and activities.
  • Understanding PDB Data, a reference to help explore and interpret individual PDB entries. Broad topics include how to understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges to exploring the archive.

PDB-101 will continue to be developed; we welcome your comments and suggestions.

To link directly to this view, use http://www.pdb.org/pdb-101.

03-May-2011

Newsletter published

The spring 2011 newsletter (HTML | PDF) highlights the upcoming PDB 40 symposium, synchrotron news, options available for exploring PDB entries, and more.

In the Education Corner, New Jersey high school teacher Richard Tempsick describes how he builds protein structures and uses the Molecule of the Month in the classroom.

The newsletter also announces new education resources for exploring the structure of the HIV virus and the results of the protein modeling event at the New Jersey Science Olympiad.

The newsletter is published quarterly online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

26-Apr-2011

Rutgers Day (April 30)

Rutgers Day (April 30).
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Rutgers Day (April 30).

Rutgers Day is a full day of discovery and lively activities that showcase the varied resources, departments, and people at the university. The RCSB PDB will be part of the Department of Chemistry and Chemical Biology's exposition on Busch Campus. Visitors will be able to build 3D DNA and virus structure models next to experiments and demonstrations of how chemistry impacts our lives.

Rutgers Day will take place from 10 a.m. - 4 p.m. rain or shine.

26-Apr-2011

New Publication

The RCSB Protein Data Bank: site functionality and bioinformatics use cases
Peter W. Rose, Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlić, Gregory B. Quinn, Benjamin Yukich, Helen M. Berman, Philip E. Bourne
NCI-Nature Pathway Interaction Database Bioinformatics Primer 10.1038/pid.2011.1

19-Apr-2011

Latest Website Release

Use the Sequence Tab to view sequence annotations in Jmol, such as the biotin binding site shown here in entry 1STP.
(Click image to enlarge)
Use the Sequence Tab to view sequence annotations in Jmol, such as the biotin binding site shown here in entry 1STP.

New and enhanced features have been added to www.pdb.org, including:

  • PDB-101, a new and unique view of the RCSB PDB that packages together the resources of interest to teachers, students, and the general public--Structural View of Biology, Educational Resources, Molecule of the Month, and Understanding PDB Data.

Clicking on the blackboard PDB-101 logo (or its related widget in the left-hand menu) reveals the education-centered website. This view offers easy navigation: select any Molecule of the Month article from the top bar menu or mouse over the PDB-101 pull-down to jump to other sections of PDB-101. Click on the blue logo in the top left at any time to access RCSB PDB deposition and query services from the main website.
For complete descriptions, see the New Features widget on the RCSB PDB home page.

  • Sequence Annotations. The sequence tab displays annotated sequences of polymer chains present in the selected structure. These annotations can be viewed in diagram form and in Jmol.

The current list of annotations includes:

  • SCOP - domain annotations from the SCOP database.
  • CATH - domain annotations from the CATH database.
  • Domain Parser - domain annotations processed with the Domain Parser (DP) algorithm
  • Protein Domain Parser - domain annotations processed with the Domain Parser (DP) algorithm
  • PFAM - regions with Pfam annotations
  • Interpro - regions with Interpro annotations
  • DSSP - secondary structure assignment
  • STRIDE - secondary structure assignment
  • Author Sec. Struc. - secondary structure assignment as provided by the author of a PDB entry
  • NEW: Protein Modification - protein modifications as detected with software
  • NEW: Site Record - both author assigned and software-detected binding sites
  • NEW: Single Nucleotide Polymorphism (SNP) - data from the LS-SNP database

  • Advanced Search: Advanced search can be used to build complex queries using multiple constraints. New query options include protein modifications, Pfam ID, and EM structures with experimental data.

For complete descriptions of all new features, see the What's New page.

12-Apr-2011

Narrated RCSB PDB Tutorial Updated

A comprehensive suite of RCSB PDB training materials is available at openhelix.com.

The updated training tools reflect many recent enhancements to the RCSB PDB site, including the data drill-down and data summary feature, updated ligand features such as a download page, images and binding affinity data, and new report types and visualization options.

The full tutorial runs for about an hour.  Users can jump to any chapters: Introduction, Basic Searching & Browsing, Result Options, Structure Summary Page, Advanced Searching, Tools & Education, Summary, or Exercises.

The PowerPoint slides used as a basis for the tutorial, the suggested script for the slides, slide handouts, and exercises are all freely available for download and use as classroom content.

12-Apr-2011

DNA Day 2011: April 15

DNA Day 2011
The Molecule of the Month's David Goodsell and a paper model of DNA.
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The Molecule of the Month's David Goodsell and a paper model of DNA. Download your own copy from the Educational Resources section.

NHGRI's National DNA Day commemorates the completion of the Human Genome Project and the discovery of DNA's double helix. It's also a day for students, teachers, and the public to learn more about genetics and genomics. Related online resources include:

05-Apr-2011

J.P. Stevens HS Wins NJ Protein Modeling Event

At the NJ Science Olympiad, 24 high schools teams demonstrated their knowledge of proteins shown to have reprogrammed adult cells into pluripotent stem cells.

The team from J.P. Stevens High School (Edison): Andy Shi, Joet Bagga, and Sam Zhang. (Click image to enlarge)
The team from J.P. Stevens High School (Edison): Andy Shi, Joet Bagga, and Sam Zhang.


Jmol was used to build models onsite. (Click image to enlarge)
Jmol was used to build models onsite.
The RCSB PDB judges provided feedback to the students. (Click image to enlarge)
The RCSB PDB judges provided feedback to the students.


Points were awarded for `creative additions` that helped tell the story of the protein.
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Points were awarded for "creative additions" that helped tell the story of the protein.

Teams submitted hand-built 3D models of the zinc finger protein found in PDB entry 2wbu on the morning of the event. The models represented the protein backbone, with additional points awarded for structures with details that highlighted important parts of the structure (such as zinc atoms).

During the event itself, the students quickly built a model of homeobox protein Nanog (PDB ID 2kt0) and answered questions on a written exam. Teams used the Molecule of the Month, Jmol, and other resources to help prepare for this event.

RCSB PDB team members judged this competition, and met with teams at the end of the day to discuss results.

Congratulations to all participating teams--there were many great models, abstracts, and responses to the written exam. Several models received perfect scores, and the challenging exam had many strong responses. Places 4-6 were decided by tiebreak questions.

Top Protein Modeling Results

1. J.P. Stevens HS (98.75)
2. Princeton (95)
3. Livingston HS (93.5)
4. West Windsor Plainsboro South (92)
5. Hillsborough (92)
6. South Brunswick HS (92)

The final results and a video demonstrating how models are built for this competition are available at education.pdb.org.

Special thanks to our judges from the RCSB PDB (Buvaneswari Narayanan, Chenghua Shao and event organizer Christine Zardecki), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

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

For protein modeling tips and news of interest to students and educators, follow us on twitter@buildmodels.

29-Mar-2011

The Structural Biology of HIV

Interactive Flash website.
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Interactive Flash website.

The NIH is sponsoring the 25th annual meeting of discussions about the exciting progress made by structural biologists in the study of HIV from March 28-30, 2011. To commemorate this event, the RCSB PDB's David Goodsell has created an image that illustrates the structural components of the HIV virus.

Goodsell's painting of the HIV virus is available for download as a poster (14 MB). The image is also part of an interactive, online Flash website (3.6 MB) that describes the structural proteins, viral enzymes, and accessory proteins that have been revealed through 25 years of research. Clicking on a protein in the virus will reveal information about the structure and a link to the entry in the PDB.

For more information about the HIV virus, see the Molecule of the Month features on HIV protease, integrase, and reverse transcriptase.

22-Mar-2011

Quick Jmol Views

PDB entry 1k4r as seen in Jmol.
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PDB entry 1k4r as seen in Jmol.

Select View in Jmol from any entry's Structure Summary page to access the interactive viewer. Frequently-used Jmol options are available in pull-down menus and buttons, including the display style, color, and surface.

For more detailed usage, click the right mouse button to access the Jmol menu, or enter scripts into the text box. Domain assignments from SCOP, DP, and PDP can also be displayed by selecting from the list provided.

15-Mar-2011

Visit us at the San Diego Science Festival on March 26

SDSF Expo Day.

On Saturday, March 26, visitors to the RCSB PDB booth at the SDSF Expo Day will learn about the basic building blocks of life by building a model of DNA and translating its sequence into protein. They can also watch animations of 3D proteins and nucleic acids, and take home posters and other materials about these fascinating structures.

SDSF Expo Day will bring together over 135 hands-on science activities and 12 stage performances for kids of all ages. It marks the end of the San Diego Science Festival, an eight-day celebration of science and engineering organized by UC San Diego and collaborators. Visit www.sdsciencefestival.com for complete details.

Can't make it to San Diego? Build models of DNA and the dengue virus at home using these PDFs from the Educational Resources page.

15-Mar-2011

Paper Published

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlić, Gregory B. Quinn, Peter W. Rose, Chaitali Shah, Jasmine Young, Benjamin Yukich, Helen M. Berman, Philip E. Bourne
Database: The Journal of Biological Databases and Curation (2011) doi: 10.1093/database/bar003

08-Mar-2011

Depositing Structures with Ligands

Ligand Expo can also be used to check and confirm the  chemistry of a chemical component. Shown is the correct sterochemistry  for alpha-D-mannose (on the left, ID: MAN) and for N-acetyl-D-glucosamine (on the right, ID: NAG).
(Click image to enlarge)
Ligand Expo can also be used to check and confirm the chemistry of a chemical component. Shown is the correct sterochemistry for alpha-D-mannose (on the left, ID: MAN) and for N-acetyl-D-glucosamine (on the right, ID: NAG).

Ligand Expo (ligand-expo.rcsb.org) accesses chemical and structural information about all small molecule components found in PDB entries. It is based upon the Chemical Component Dictionary maintained by the wwPDB.

When depositing a structure with a ligand

  • Search Ligand Expo for a chemical component that matches your ligand
  • If a match is found, use the corresponding three-character code for the ligand in your coordinates
  • If the ligand is new, choose a new three-character code for the ligand.
  • When depositing your structure with ADIT, upload the chemical name and formula and/or a file showing the chemical image for the new ligand into the Ligand Information section

Ligand Expo can search the Chemical Component Dictionary using uploaded data files (e.g., PDB, MOL/SDF, Refmac/Phenix monomer library (mmCIF)); chemical name; formula; SMILES string; and ID code.

Searches for instances of ligands associated with macromolecular structures can also be performed at www.pdb.org using a variety of options, including the top bar Chemical Name/ID search, Advanced Search, and the Chemical Structure Search. Users can then explore the ligand structures and the related PDB entries. Online screencasts are available at the RCSB PDB site to help users explore these features.

01-Mar-2011

Upcoming Meetings

Recently, the RCSB PDB  hosted a virus model activity as part of Family Days at the AAAS meeting.
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Recently, the RCSB PDB hosted a virus model activity as part of Family Days at the AAAS meeting.

Stop by the exhibition hall at these upcoming meetings to speak with team members, explore new website features, and to pick up the How Do Drugs Work? poster and other materials.

At the Biophysical Society meeting (March 5-9, Baltimore, MD), the RCSB PDB and SBKB will exhibit in stand 843.

At the national conference of the National Science Teacher Association's meeting (March 10-13, San Francisco), the RCSB PDB will highlight educational materials and features at stand 833.

22-Feb-2011

Structural Neighbors

Comparison of 1q6z (orange) with structural neighbor 3hww (cyan).
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Comparison of 1q6z (orange) with structural neighbor 3hww (cyan).

Proteins can have various degrees of similarity. If two proteins have highly similar amino acid sequences, it is generally assumed that they are closely related evolutionarily. As the evolutionary distance increases, the degree of similarity usually drops. Even if the sequence similarity is low, proteins may have similar functions and 3D structures. Detecting remote similarities, a core structural bioinformatics technique, is important in the study of functional and evolutionary relationships between protein families.

The RCSB PDB offers tools that quickly identify 3D protein sequence neighbors. For each PDB entry, the 3D Similarity tab lists the representative entries with 40% sequence similarity that are found using the jFATCAT-rigid algorithm. As an example, look at the 3D similarity tab for entry 1q6z. Representative protein chains are used since calculation of a real all vs. all comparison would require a great amount of CPU time. A detailed description of the procedure used is available.

Novel domain architectures and unexpected structural similarities can be detected by analyzing structural alignments. As an example, one of the top ranking structural neighbors of 1q6z (chain A), is entry 3hww. Clicking on "view" from the Structure Similarity table will show a summary view of the alignment.

3hww has an RMSD of 3 Å based on the Cα positions, while the two protein chains are only 14% identical by sequence. 1q6z is a benzoylformate decarboxylase (EC number 4.1.1.7), while 3hww is a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (EC number 2.2.1.9). Despite the low sequence identity and divergence in function, the high structural similarity indicates that both proteins evolved from a common ancestor.

15-Feb-2011

Upcoming Meeting: AAAS Meeting and Family Days

RCSB PDB and SBKB will promote molecular explorations of biology at the AAAS Annual Meeting (Feb 17-21, Washington DC).

Exhibit Booth #733 will demonstrate A Structural View of Biology at the 2011 meeting of the American Association for the Advancement of Science.

Hands on activities will also be available for students attending the meeting's Family Science Days.

08-Feb-2011

Create High Resolution Images

Image of 3izi created using Protein Workshop.

(Click image to enlarge)
Image of 3izi created using Protein Workshop.

The RCSB PDB website offers interactive, Java-based tools1 to visualize PDB data. Protein Workshop offers easily customized views; Simple Viewer offers a quick ribbon display; and Ligand Explorer visualizes the interactions of bound ligands in protein and nucleic acids structures.

The 'Save Image' dialog box.

(Click image to enlarge)
The 'Save Image' dialog box.

Journals often require figures in a particular size and print resolution (typically 300 or 600 DPI). We have recently added a new feature to our 3D viewers to save custom high-resolution images in the JPEG, PNG, and TIFF formats. Using the Save Image dialog box from the File menu, users can specify the print resolution in DPI (dots per inch), the width and height of an image in pixels, inches, or millimeters.

1. J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications BMC Bioinformatics 6:21.

01-Feb-2011

Store Personal Annotations With MyPDB

Store Personal Annotations With MyPDB.

MyPDB lets users create a personalized version of the RCSB PDB that is accessible from any computer and from PDBMobile.

The starting point is the MyPDB widget in the left-hand menu. Users can create new accounts, or log in to access MyPDB functionalities.

  • The MyPDB Saved Query Manager stores any type of RCSB PDB structure search, such as keyword, sequence, ligand, and any composite query built with Advanced Search. These queries can be run at any time with the click of a button.

Stored searches can also be set to run with each update. Email alerts (weekly or monthly) will be sent when new PDB entries matching the search are released.

  • Personal Annotations. Users can save personal annotations and notes on the Structure Summary tab of any PDB entry, and can add structures to a "favorites list". The Personal Annotations summary page provides easy access to all of these tagged structures and annotations.

  • User Account. Personal information (name, email address, account password, country, user type) can be updated at any time. All MyPDB account information is kept private and secure.

25-Jan-2011

NJ Science Olympiad Protein Modeling Results

West Windsor Plainsboro South (Team 2) and their prebuild model of  2wbu.
(click to enlarge)
West Windsor Plainsboro South (Team 2) and their prebuild model of  2wbu.


Teams built a portion of  PDB entry 1gt0 using Jmol during the competition.
(click to enlarge)
Teams built a portion of  PDB entry 1gt0 using Jmol during the competition.

48 teams from high schools in New Jersey demonstrated their understanding of protein structure and stem cells at three regional Science Olympiad competitions.

The competition focused on proteins that have been shown to reprogram adult cells into pluripotent stem cells.  Teams were judged by the RCSB PDB on their knowledge of protein structure and function based upon a protein model of PDB entry 2wbu built before the competition, a model quickly built at the competition of a portion of PDB entry 1gt0, and a written exam.

RCSB PDB team member Huangwang Yang awarded points for models that illustrated the protein's function.
(click to enlarge)
RCSB PDB team member Huangwang Yang awarded points for models that illustrated the protein's function.

The top scoring teams were:

Southern (January 8)
1. Cherry Hill East (85 points)
2. JP Stevens (Team 2, 84)
3. Lawrenceville (81)

Central (January 11)
1. Hillsborough (88.5)
2. Westfield (86)
3. Union County Vo-Tech (83)

Northern (January 14)
1. West Windsor-Plainsboro HS South (Team 2, 95.5)
2. West Windsor-Plainsboro HS South (Team 1, 91)
3. Livingston (88.5)

Full results are posted online.  Information and resources about this NJ event are posted at education.pdb.org and on Twitter at @buildmodels.

Protein modeling will be one of several events at Science Olympiads across the country. Teams are recognized for their performance in individual events and in the overall tournament. For more information, see http://cbm.msoe.edu/stupro/so/index.html.

Many thanks to the RCSB PDB judges (Batsal Devkota, Brian Hudson, Buvaneswari Narayanan, Chengua Shao, Huangwang Yang, and Christine Zardecki), the NJ Science Olympiad organizers and volunteers, the host colleges, and to the MSOE Center for BioMolecular Modeling for the materials and design of this event. We look forward to seeing everyone at the state finals in March!

18-Jan-2011

Newsletter published

Winter 2011 Newsletter.

The winter 2011 issue (HTML | PDF) looks at the year 2010 through data deposition, website traffic, and Molecules of the Month.  It also highlights the latest website release, recent meeting activities, the 2010 Annual Report PDF, and more.  In the Education Corner, Jaime Prilusky (Weizmann Institute of Science) gives an overview of Proteopedia: An online, collaborative 3D-encyclopedia of proteins & other molecules.

The newsletter also has announcements regarding a Quick Survey on the Educational Uses of Molecular Visualization, and the NIH's 25th Annual Meeting on HIV/AIDS-related Structural Biology.

The newsletter is published quarterly online and in print. To request the printed version, please send your mailing address to info@rcsb.org. Subscription information for the electronic version is available.

11-Jan-2011

Papers Published

An introduction to the PDB for undergraduates, an overview of the RCSB PDB website, and an article on the Comparison Tool have been published.

A list of all RCSB PDB articles is available from the News & Publications page.

04-Jan-2011

Structural Biology Knowledgebase Widget

Structural Biology Knowledgebase Widget.
(click to enlarge)
Structural Biology Knowledgebase Widget.

The Structural Biology Knowledgebase (SBKB) is a free, comprehensive resource that integrates the results of structural biology and genomics efforts with other publicly available biological information to facilitate further research. A new widget on every RCSB PDB Structure Summary page links to the related information at the SBKB. It asynchronously loads data about available models, protein targets, related biological annotations, related clones and protocols with links to SBKB reports page.

The SBKB is part of the Protein Structure Initiative:Biology Network and funded by NIGMS.