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Year 2010 News

Contents:

28-Dec-2010 Happy Holidays
21-Dec-2010 Deposition Session Restart IDs
14-Dec-2010 Annual Report Published
07-Dec-2010 Latest Website Release
07-Dec-2010 Poster Prize Awarded at AsCA
30-Nov-2010 Learn About Viruses
30-Nov-2010 New and Improved Web Services for Accessing PDB Data
23-Nov-2010 New Ligand Summary Pages
16-Nov-2010 Explore Search Results Using Data Distribution Summaries
09-Nov-2010 Creating Tabular Reports
02-Nov-2010 PDBMobile
26-Oct-2010 Newsletter Published
19-Oct-2010 Binding Affinity Data Integrated with RCSB PDB
12-Oct-2010 Categorized View of Molecule of the Month
05-Oct-2010 Latest Website Release
28-Sep-2010 Poster Prize Awarded at ECM
28-Sep-2010 Analyze small molecule interactions in the PDB with Ligand Explorer
21-Sep-2010 Redesigned BioSync
14-Sep-2010 Exploring Search Results
07-Sep-2010 Tools for Education
31-Aug-2010 Newsletter Published
24-Aug-2010 New Flyers Available
24-Aug-2010 Poster Prize Awarded at ACA
17-Aug-2010 Upcoming Meeting: PDB Symposium at ACS
10-Aug-2010 ADIT 2.0 Offers Improved Deposition Process
10-Aug-2010 wwPDB News: Validation Report PDFs
03-Aug-2010 Poster Prize Awarded at ISMB
27-Jul-2010 Looking at Structures: A Resource for Learning About PDB Data
27-Jul-2010 Paper Published
20-Jul-2010 Upcoming Meeting: ACA
20-Jul-2010 New Release of pdb_extract Available Online and for Download
13-Jul-2010 Get the Latest wwPDB News
06-Jul-2010 ISMB and 3DSIG Meetings
06-Jul-2010 Improved Version of ADIT Available
29-Jun-2010 Use Ligand Expo When Depositing Structures with Ligands
29-Jun-2010 Version 2 NMR Restraint Files Available from the wwPDB FTP
22-Jun-2010 Latest Structures Widget
15-Jun-2010 Papers published
08-Jun-2010 New Website Features
08-Jun-2010 Improved Version of ADIT Available, Transitional Implementation Starts June 14
01-Jun-2010 Create a Collage of Structures
25-May-2010 Search the RCSB PDB in Your Web Browser
18-May-2010 Turn Your Computer into a PDB Structure Kiosk
11-May-2010 New Website Features and Widgets
04-May-2010 wwPDB To Provide Validation Reports as PDFs
04-May-2010 Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010
27-Apr-2010 Newsletter Published
20-Apr-2010 Screencasts Demonstrate RCSB PDB Features
20-Apr-2010 DNA Day: April 23
13-Apr-2010 Exhibiting at Experimental Biology (April 24-28)
13-Apr-2010 Come build virus models at Rutgers Day (April 24)
06-Apr-2010 Bookmark and Share RCSB PDB Webpages
30-Mar-2010 Advanced Search: Sequence Motif
23-Mar-2010 West Windsor Plainsboro High School North Wins New Jersey Science Olympiad Protein Modeling State Finals
23-Mar-2010 San Diego Science Festival Expo Day: March 27
16-Mar-2010 Exhibiting at NSTA
09-Mar-2010 Improved Ligand Searching
02-Mar-2010 New Website Features
23-Feb-2010 Online Narrated Tutorial Demonstrates How to Use the RCSB PDB
23-Feb-2010 Changes to the wwPDB Policy for Depositing Polypeptide Structures
16-Feb-2010 Exhibition at the Biophysical Society Meeting
09-Feb-2010 Poster Download: How Do Drugs Work?
02-Feb-2010 Newsletter Published
02-Feb-2010 wwPDB FTP Advisory Notice
26-Jan-2010 Comparison Tool for Exploring Sequence and Structure Alignments
19-Jan-2010 NJ Science Olympiad Protein Modeling Results
12-Jan-2010 Time-stamped Copies of PDB Archive Available via FTP
05-Jan-2010 2009 Annual Report Published

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


28-Dec-2010

Happy Holidays

Happy Holidays.
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Image of lumazine synthase fromPDB ID 1hqk.

Best wishes for a wonderful new year!

For some RCSB PDB highlights from the past year, be sure to download the 2010 Annual Report (PDF).

21-Dec-2010

Deposition Session Restart IDs

ADIT 2.0 can launch an email message that contains a deposition session's restart ID.

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ADIT 2.0 can launch an email message that contains a deposition session's restart ID.

Depositing a PDB entry can take place over a period of time using ADIT's "Session Restart ID" feature. Each deposition session has a single ID that can be emailed to the depositor and used to restart the session at a later date.

After initially uploading files, ADIT 2.0 runs checks for data format, validation, and sequence.  On each of these pages, select "Click here to e-mail the session restart ID" to send an email containing the restart ID.

This identifier also appears in the title and the initial center panel of the ADIT editor window.

The unique case-sensitive restart ID, a combination of the date, time, computer IP, and session number, is generated automatically.  It should be entered in the space provided on the ADIT home page to return to the deposition session.  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.


14-Dec-2010

Annual Report Published

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The cover illustration represents the new categorized view for navigating through the archive of Molecule of the Month columns. Each structure shown represents a major, top-level functional category that can be browsed through descriptive subcategories that lead to individual features.

Download the 2010 Annual Report (PDF) for an overview of the RCSB PDB resource and its recent activities.

Since 2000, the Annual Report has provided yearly snapshots of the project.  With this year's edition, printed reports will not be mailed directly to users.  

Aimed at the RCSB PDB's diverse community of PDB users in academia, industry, and education, the report highlights recent accomplishments in the report period of July 1, 2009 - June 30, 2010. It explores the RCSB PDB's different activities in "data in" (data deposition, validation, and annotation), "data out" (data access, query, and reporting), and corresponding outreach and education activities.

07-Dec-2010

Latest Website Release

New and enhanced features have been added to www.pdb.org, including:
 
* MyPDB storage of annotations on particular PDB entries.  Log in, view a Structure Summary page, and make a note in the MyPDB Personal Annotations Widget.  That message will appear on that page, and on your MyPDB Personal Annotation summary page every time you log in.

* Access to Transporter Classification information.  Browse membrane transport proteins in the PDB archive using the Transporter Classification (TC) system from the Transporter Classification Database (www.tcdb.org).

* New data distribution summaries for search results.  Pie charts are now available to explore query results by SCOP and Enzyme Classification number. Users can use these drill-down options, or 'faceted search' options, to quickly access a set of structures. Any combination of categories is possible.
 
* Access to data from the Structural Biology Knowledgebase.  From an entry's Structure Summary page, users can see the related models, protein targets, biological annotations, clones and more as provided by the SBKB.

* High-resolution Image Generation.  Simple Viewer, Protein Workshop, and Ligand Explorer have a new option to save high-resolution images in JPEG, PNG, and TIFF formats.

For complete descriptions, see the New Features widget on the RCSB PDB home page.

07-Dec-2010

Poster Prize Awarded at AsCA

Poster prize winner Takuya Yoshizawa.
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Poster prize winner Takuya Yoshizawa.

Takuya Yoshizawa received the poster prize at the 10th Conference of the Asian Crystallographic Association held in Busan, Korea (October 31 - November 3) for Crystal structures of extra cellular dermal glycoprotein from carrot and xyloglucan specific endo-b-1,4-glucanase from Aspergillus aculeatus by Takuya Yoshizawa1, Hiroshi Hashimoto1, Toshiyuki Shimizu2, Hisashi Hirano1 and Mamoru Sato1 (1Graduate School of Nanobioscience, Yokohama City University; 2Graduate School of Pharmaceutical Sciences, The University of Tokyo).

Many thanks to the judges: Eunice Kim (Korea Institute of Science and Technology), Kunio Miki (Kyoto University), Zhi-Jie Liu (Institute of Biophysics, Chinese Academy of Sciences) and Soo Hyun Eom (Gwangju Institute of Science and Technology), and to Mitch Guss, Jenny Martin, and the Asian Crystallographic Association.


30-Nov-2010

Learn About Viruses

Image of the dengue virus from the Molecule of the Month.
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Image of the dengue virus from the Molecule of the Month.

For the Howard Hughes Medical Institute's (HHMI) 2010 Holiday Lectures, leading virus researchers Joe DeRisi and Eva Harris will discuss Viral Outbreak: The Science of Emerging DiseaseInformation about the live and on-demand webcasts is available.

For related information on the 3D structures of viruses, see the RCSB PDB's Molecule of the Month features on viruses, including the dengue virus, build a 3D paper model of the dengue virus (PDF), and explore related lesson plans.

30-Nov-2010

New and Improved Web Services for Accessing PDB Data

Web Services can help software developers build tools that interact more effectively with PDB data. Instead of storing coordinate files and related data locally, web services let software tools interact with the RCSB PDB remotely. Documentation for accessing the RCSB PDB's Web Services is available (RESTful | SOAP).

RESTful services exchange XML files in response to URL requests. RESTful search services return a list of IDs for Advanced Search and SMILES-based queries. RESTful fetch services return data when given IDs, including PDB entity descriptions, ligand information, third-party annotations for protein chains, and PDB to UniProtKB mappings. SOAP Web Services are also available.

Improvements are being made based on community feedback. Please let us know if there are website options that you think should be offered as a web service.  

23-Nov-2010

New Ligand Summary Pages

Ligand Summary Pages provide information for all of the entries found in the wwPDB`s Chemical Component Dictionary.
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Ligand Summary Pages provide information for all of the entries found in the wwPDB's Chemical Component Dictionary.

Similar to Structure Summary pages for PDB entries,  Ligand Summary Pages use a widget framework to highlight different types of information about the small molecule components found in PDB entries.  These entries can be accessed by performing a ligand search, selecting a ligand from a PDB entry's Structure Summary page, and from the Ligand Hits tab for query results.

For example, view the Ligand Summary Page for HEM.

A Chemical Component Summary provides an overview of the structure, including name, identifiers, synonyms, and SMILES and InCHI information.

A Related Entries widget links to all PDB entries where the ligand appears as a polymeric residue, a free ligand, or both.

The Related Ligands widget links to summary pages for similar ligands and stereoisomers, and automatically enters the ligand in the RCSB PDB's Chemical Structure Search to build related ligand searches.

Toggle between a static image and a 3D Jmol view using the Ligand Image widget.

The Links widget lets users explore information related to the same chemical component at external resources (BindingDB, HIC-Up, PDBeChem and more) and the RCSB PDB's Ligand Expo.

For more information on this feature and other recent enhancements to the website, see the What's New page.

16-Nov-2010

Explore Search Results Using Data Distribution Summaries

Search results organized by organism.

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Search results organized by organism.

RCSB PDB search results offer summary pie charts and summary links for standard characteristics of PDB entries (resolution, release date, experimental method, polymer type, organism, taxonomy) that can be used to refine search results into subsets of interest. For example, users can use these drill-down options, or 'faceted search' options, to quickly access high resolution entries from a structure type search; human-related entries from a sequence search; or most recent entries resulting from a chemical component search. Any combination of categories is possible.  These charts can be hidden for users who only want to view the individual entries.

Data distribution summaries can also be used to explore the latest weekly update of PDB entries or the entire PDB archive by clicking on the date of the latest release or the number of structures in the archive listed in the top menu bar.

For more information on this "drill-down" feature, and other recent enhancements to the website, see the What's New page.

09-Nov-2010

Creating Tabular Reports

The `Generate Reports` pull-down menu.
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The Generate Reports pull-down menu.

Tabular reports offer a convenient ways to view, export, and interact with query results. 

What types of reports are available?
After entering a search, select the Generate Reports pull-down menu on the Structure Hits tab to create a tabular report for the set of returned structures.  In addition to creating a collage of structure images, users can generate:

  • A customized table created by selecting combinations of fields, including experimental, structural, and non-structural data; references to sequence databases (UniProtKB , Pfam), domain information (CATH, SCOP); literature (PubMed); and ontology terms (GO, MeSH)
  • Pre-generated summary reports about structure, sequence, ligand, literature, and biological details
  • Pre-generated experimental reports specific for X-ray or NMR structures

From the Ligand Hits tab, select Generate Reports>Ligand Results Table to generate a table that includes the ligand ID, image, formula, molecular weight, name, SMILES, and the PDB IDs for the related entries.

How can tabular reports be customized?
The interactive interface for tabular reports can be used to create different views of the query results.

Example Structure Summary tabular report .
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Example Structure Summary tabular report that was customized by selecting the columns to be displayed, using the inline filter to limit the results to structures with experimental method `X-RAY`, and sorting by resolution. Up to 1000 rows per page can be displayed.
Users can:
  • Sort the table by column (click on column header)
  • Quickly refine the query results by using the inline filter (type text in box below column header)
  • Further refine the results set by using the Advanced filter to combine multiple conditions (Filter Results link)
  • Show/hide columns and change column order (Customize Columns link)
  • Adjust column width (drag column separator)
  • Change number of results per page (bottom menu bar)
  • Resize table (drag bottom right corner of table)

In which formats can the data be exported?
Select one of the icons below to download the report in:

  • Excel 97-2003 format: Multiple work sheets will be generated for large data sets to accommodate the row limitation (65,536) in older versions of Excel.
  • Excel 2007 or newer versions
  • CSV: Comma Separated Value format (no limitations, recommended for extra large data sets)

Export in Excel is limited to 1,000,000 cells (#rows * #columns). Larger reports can be export in the CSV format. The Excel spreadsheets have been reformatted with customized column width, text wrapping, alignment, and hyperlinks on selected columns. Previous formatting issues with PDB IDs appearing as floating point numbers (e.g., such as 1E10) have been resolved.
A detailed description of the tabular reports is available.

02-Nov-2010

PDBMobile

PDBMobile (Version 1.0) lets users access RCSB PDB features and functionality on iPhones and iPods.  Users can read the Molecule of the Month and the latest news and announcements, search the database and browse  results, and access MyPDB accounts.

A new feature of MyPDB is being tested with PDBMobile.  Users can type and  store personal annotations for any PDB entry in their MyPDB account. Annotations are made by flipping over the entry abstract pane and typing into the text area.

PDBMobile is an HTML5-based application for mobile devices that initially targets iPhone and iPod devices.  Future releases will target other platforms. 

See the installation screencast and the PDBMobile FAQ for more information.  



26-Oct-2010

Newsletter Published

The fall 2010 issue (HTML | PDF) highlights the latest website release, a new version of pdb_extract, structural genomics in the news, and more.  In the Education Corner, Joan Kiely (Stony Brook University) describes the Protein Challenge, a protein building competition for high school students.

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.

19-Oct-2010

Binding Affinity Data Integrated with RCSB PDB

Binding affinity data from BindingDB have been integrated with the RCSB PDB website. The Ligand Chemical Component section of Structure Summary pages now include binding affinity data from BindingDB, when available (for an example, see an HIV-1 protease dimer complexed with Ritonavir in entry 1hxw). These include binding constants IC50, EC50, Ki, and thermodynamic data Kd, ΔG, ΔH, -TΔS. If multiple experimental values are available for a measurement type, a range is listed. The data are linked to the BindingDB resource.

A new Advanced Search option can be used to find protein-ligand complexes with associated binding affinity data. IC50, EC50, Ki, and Kd must be specified in nM, and thermodynamic data ΔG, ΔH, -TΔS in kJ/mol. To use this option, select the "Binding Affinity" option from under Chemical Components in Advanced Search.

For information about this and other new features, please see the What's New page.

12-Oct-2010

Categorized View of Molecule of the Month

Categorized Views.

Currently, 130 Molecule of the Month articles cover topics from AAA+ proteases to zinc fingers. These columns have been organized to help users explore the Molecule of the Month--and the PDB archive--in the context of biology.  Major functional categories can be browsed for areas of interest. Within each topic, descriptive subcategories then lead to the relevant Molecule of the Month features. These categories will grow as new features are published.

The major topic categories include:

Past Molecule of the Month articles can still be searched by date and feature title, but the category view lets users access the Molecule of the Month archive with a biological interest in mind, rather than a specific molecule.  The Biological Energy topic category, for example, contains subcategories Capturing the Energy in Food, Photosynthesis, Molecular Motors, and Creating and Capturing Light, which can be browsed for the related Molecule of the Month features.  The same article will be listed under multiple categories/subcategories if it can be categorized in several ways.

Questions, comments, and suggestions are welcome at info@rcsb.org.

05-Oct-2010

Latest Website Release

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

* Improved navigation of Molecule of the Month archive: new category views and a new sortable table to view features by category, date and name.

* PDBMobile for the iPhone: search the RCSB PDB, browse results, access MyPDB, and read the latest news and Molecule of the Month features.
PDBMobile is an HTML5-based application for mobile devices. It initially targets iPhone and iPod devices running iOS4. Future releases will target other platforms, including the iPad, Google Android and Windows Phone 7.

* New ways to explore search results using data distribution summaries. Search results now offer summary charts for standard characteristics of PDB entries (resolution, release date, experimental method, polymer type, organism, taxonomy) that can be used to refine search results into subsets of interest. For example, users can use these drill-down options, or 'faceted search' options, to quickly access high resolution entries from a structure type search; human-related entries from a sequence search; or most recent entries resulting from a chemical component search.  Any combination of categories is possible.

* Integration with Binding Affinity Data from BindingDB (www.bindingdb.org). The Ligand Chemical Component widget on a Structure Summary page lists and links to binding affinity data from BindingDB (when available).

* New Help features, including a sitemap and glossary.

For complete descriptions, see the New Features widget on the RCSB PDB home page.

28-Sep-2010

Poster Prize Awarded at ECM

Sven Dahms.

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Sven Dahms.

Sven Dahms received the poster prize at the 26th European Crystallographic Meeting held in Darmstadt, Germany (August 29 - Sept 2) for Structure and biochemistry of the APP E2-domain by Sven O. Dahms, Dirk Roeser, Manuel E. Than (Fritz Lipmann Institute, Jena, Germany).

Many thanks to the judges: Wolf-Dieter Schubert (Helmholtz Centre for Infection Research) and Norbert Straeter (University of Leipzig), and to Andreas Roodt, Petra Bombicz, and the European Crystallographic Association.


28-Sep-2010

Analyze small molecule interactions in the PDB with Ligand Explorer

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

Ligand Explorer can display hydrogen bonds, hydrophobic interactions, bridged H-bonds, metal interactions, and neighbor residue interactions and thresholds in a dynamic viewer.

Users can 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 an image file, or as a text file listing interactions. 

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.

21-Sep-2010

Redesigned BioSync

Biosync logo.

Biosync (biosync.sbkb.org) is the structural biologist's online guide to high energy data collection facilities.  As data collected from synchrotron beamlines currently account for more than 80% of all X-ray crystallographic entries deposited to the PDB, the BioSync resource has been recently upgraded with a new layout and features.  BioSync provides detailed information about the state-of-the-art in macromolecular synchrotron facilities, and compiles statistics about the information collected at the beamlines.

To explore BioSync, select one of the options from the top menu bar:

* Information about each synchrotron is organized by location (Americas, Europe, and Asia/Oceania).  Data sheets for operational macromolecular beamlines at synchrotrons worldwide describe available services and functions (new additions include remote data collection; mail-in, crystallization and structure solution services; robotics handling for crystal screening and mounting; microfocus beams and facilities for collecting data under extreme conditions).  Users can also search for specific capabilities, services and equipment across beamlines. Beamline information is uploaded by synchrotron personnel.

* Deposition Statistics are grouped by synchrotron and by geographical region. Site statistics are broken down to the beamline level; new graphs compare beamlines within a site. Galleries of structures and tables containing citations and other general information (e.g. phasing methods, wavelength used for data collection, resolution, R-factors, numbers of atoms) are also available. A separate set of statistical tables, galleries and informational tables is provided for structures produced by structural genomics efforts.

* Simple and Advanced Search options are available.  Simple searches look for synchrotrons by name or location; a new feature can return a breakdown of structure counts per country for a site or a single beamline.  The Advanced Search option can be used to look for more detailed beamline features and services.

The redesign and upgrade of BioSync was funded by NIGMS.  Questions? Email biosync@sbkb.org.

14-Sep-2010

Exploring Search Results

Search results.

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Search results.

The streamlined Query Results page displays information about each entry returned in any search in an easy-to-read layout.

Summary information about each structure helps users decide which entries will be explored further.  Polymer details,  ligand information and illustrations, and the citation abstract can be expanded and condensed.

By default, the most recently released entries are shown at the top.  The structures shown can be sorted by release date, residue count, or resolution, and number of entries displayed on a page can be increased.

Each individual entry on this page has links to the related Structure Summary page, PDB file, and Jmol view.

The set of structures returned in a query can be further refined or modified using Advanced Search functionality, or can be reduced to a subset of structures by using a sequence similarity cutoff.

The entire set of structures, or a subset of these structures, can be selected to download all PDB data files or to be included in a tabular report.

07-Sep-2010

Tools for Education

The RCSB PDB offers resources for teachers  and students; many are described in the recently-published  "Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences" (J. Appl. Cryst. (2010). 43   doi:10.1107/S002188981002371X).

 Accessible from the left hand menu, the RCSB PDB's Education section offers:

  • Understanding PDB Data: Through text, images, and interactive Jmols, this feature 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.
  • Educational Resources: This page archives many of the educational materials created by the RCSB PDB, including animations, handouts, and more.  Recent additions include an updated edition of  the Bioinformatics of Green Fluorescent Protein tutorial guide (PDF) and the How Do Drugs Work poster (PDF) and flyer (PDF).
  • RCSB PDB Newsletters and Education Corner:  Published quarterly, the newsletter describes new developments, outreach efforts, and interviews with leaders in the community.  The newsletter's Education Corner, which highlights how the PDB is used in different facets of education, are also archived on a single page.  Past Education Corners have featured a rubric for biomacromolecular 3D literacy, the program Molecules for the iPhone, and physical 3D models of molecules.
  • Molecule of the Month: Each Molecule of the Month installment includes an introduction to the structure and function of a particular molecule, a discussion of the relevance of the molecule to human health and welfare, suggested additional readings and resources, and interactive views.

For an introduction to the features and functionality of the RCSB PDB website, comprehensive training materials are available at openhelix.com. The training tools include

  • An online narrated tutorial that demonstrates basic and advanced searching, report generation, exploring individual structures, and many other research and education tools.
  • The animated PowerPoint slides from the tutorial
  • Slide handouts and exercises
  • Quick Reference Cards that highlight search strategies, features and functionality. The cards can be ordered at openhelix.com at no cost; shipping is free within the United States.

Short, online narrated videos describe how to use ligand searching and website customization tools.  The screencasts currently offered at the RCSB PDB site demonstrate:

  • Ligand searching: Using the MarvinSketch applet
  • Ligand searching: Advanced MarvinSketch features
  • Ligand searching: Using SMARTS features
  • Ligand searching: Loading a PDB chemical component
  • Customizing Structure Summary pages using Widgets
  • Tour of the left hand menu

Other educational resources are described in a downloadable flyer (PDF).

31-Aug-2010

Newsletter Published

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The summer 2010 issue (HTML | PDF) describes new website features (including new home page widgets, OpenSearches of the RCSB PDB, and improved ligand searching), the wwPDB's PDF validation reports,  the release of ADIT 2.0, and more.

In the Education Corner, Phil McFadden (Oregon State University) describes Protein Portraits, a nontraditional college course developed around the question of what it might be like to shrink to the nanometer realm for a direct encounter with a protein molecule. The sculptures created as part of this class are shown.

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.

24-Aug-2010

New Flyers Available

New Flyers Available.

The RCSB PDB publishes news, tutorials, screencasts, guides, and more electronically. New printed materials are also distributed at the RCSB PDB's exhibit booths at professional society meetings.

These flyers describe resources of interest to data depositors (pdb_extract, sugar geometry), data users (Comparison Tool, Ligand Searching, Widgets), educators (Educational Resources) and more.

Information is also available about related resources, including the wwPDB (Validation Reports and RSS Feed), the beta version of the BioSync Guide to Synchrotron Facilities, and the Electron Microscopy Data Bank.

For a customized packet of flyers and information for your lab or department, please send your postal address and user type (depositor, users, educator, all) to info@rcsb.org.

24-Aug-2010

Poster Prize Awarded at ACA

Poster prize winner Serah Kimani.
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Poster Prize Awarded at ACA

The RCSB PDB Poster Prize at the 2010 Meeting of the American Crystallographic Association (ACA, July 24-29; Chicago, IL) went to Serah Kimani for Catalysis in the nitrilase superfamily amidases: Insights from the active site (Serah Kimani(1), Brandon Weber(2), Andrew Nel(3), Don Cowan(3), Trevor Sewell(2). (1)Molecular and Cell Biology Department, University of Cape Town, Western Cape, South Africa, (2)Electron Microscope Unit, University of Cape Town, Western Cape, South Africa, (3)Department of Biotechnology, University of the Western Cape, Western Cape, South Africa).

Sereh, who also won the award in 2007, will receive two educational books.

Honorable mentions were

  • Yuan Cheng, A uniquely open conformation revealed in the structure of a novel protein arginine Methyltransferase (Yuan Cheng, Monica Frazier, Matthew Redinbo University of North Carolina at Chapel Hill)
  • Jennifer Cash, The structure of the muscle growth inhibitor myostatin bound to follistatin 288:  Insights into receptor utilization and heparin binding (Jennifer Cash(1), Carlis Rejon(2), Alexandra McPherron(3), Daniel Bernard(2), Thomas Thompson(1). (1)University of Cincinnati (2)McGill University, (3) National Institutes of Health

Many thanks to the judges: Michael James (University of Alberta), Cheryl Klein Stevens (Xavier University), Bi-Cheng Wang (University of Georgia), Eric Ortlund (Emory University), and Charles Carter (University of North Carolina at Chapel Hill).  Thanks also to Poster Committee Chair Victor G. Young, Jr. (University of Minnesota) and to Marcia Colquhoun and the ACA.

17-Aug-2010

Upcoming Meeting: PDB Symposium at ACS

ACS logo.

On Sunday, August 22 at 1:30 p.m.,  The PDB and Chemistry symposium will be held as part of the American Chemical Society's Fall National Meeting (Boston Convention & Exhibition Center, Room 157C).

Symposium presenters will explore all aspects of the chemical components found in the PDB  archive:

  • wwPDB: An organization that provides macromolecular structural data to the global community (Helen M. Berman, RCSB PDB)
  • The wwPDB Common Annotation and Deposition Tool project (Martha Quesada, RCSB PDB)
  • Small molecule resources and search tools at the PDB (John Westbrook and Dimitris Dimitropoulos, RCSB PDB)
  • Remediation of PDB entries containing molecules with antibiotic and inhibitory pharmacological properties (Kim Henrick, PDBe)
  • The synergies of the PDB and the CSD (Tjelvar S.G. Olsson, CCDC)
  • Iridium: prepping PDB data for use in computation chemistry software development (Greg Warren, OpenEye)
  • Challenges in positioning, validation, annotation and visualization of chemical compounds bound to proteins (Ruben Abagyan, UCSD)

A presentation on Using molecular structures from the PDB for a visual and exploratory learning experience in biochemistry will be part of the Advances in Teaching afternoon session on Tuesday, August 24 from 1:30 p.m. - 5:15 p.m. in the Seaport Hotel Ballroom A.

10-Aug-2010

ADIT 2.0 Offers Improved Deposition Process

The ADIT deposition tool logo

A new and improved version of ADIT, a tool for validating and submitting structures to the PDB archive, has been released.

ADIT 2.0 indicates file format errors and provides suggestions for solutions; automatically runs validation checks; and reviews the consistency between sequence and coordinates. Improved help information and documentation are provided. The forms for entering sequence information, structure title, author names, and citation information have also been streamlined.

This version of ADIT was developed based on user feedback and suggestions, and implemented after a period of testing.

ADIT and its related tools are available from deposit.rcsb.org. Deposition sessions currently in process will not be disrupted; depositors will not have to update any bookmarks or session ID.

10-Aug-2010

wwPDB News: Validation Report PDFs

WWPDB logo.
(reprinted from wwpdb.org)

wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking as part of the structure annotation process. These documents are available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site (Example reports: RCSB PDB | PDBe | PDBj). The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures.

PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process and are described in an editorial recently published in Nature Structural & Molecular Biology

Questions about these reports and the annotation process may be sent to info@wwpdb.org.


03-Aug-2010

Poster Prize Awarded at ISMB

RCSB PDB Poster Prize winner Mickey Kosloff.

(Click image to enlarge)
RCSB PDB Poster Prize winner Mickey Kosloff.

The RCSB PDB Poster Prize at the 18th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB, July 11-13; Boston, MA) went to Mickey Kosloff for Structure-based redesign of selective G-protein inactivation by RGS proteins (Mickey Kosloff, Amanda M. Travis and Vadim Y. Arshavsky, Duke University Medical Center). Mickey will receive two educational books for the award. 

Many thanks to the judges: Manisha Brahmachary, Brian Chen, Fabian Dey, Markus Fischer, Tobias Hamp, Laszlo Kajan, Eugenia Lyashenko, Marco Punta, Shruti Rastogi, Ta-tsen    Soong (Columbia University), Avner Schlessinger (University of California San Francisco), and Mikhail Dozmorov (Oklahoma Medical Research Foundation). Thanks also to Poster Committee Chair Yana Bromberg (Columbia University) and to the International Society for Computational Biology.


 

27-Jul-2010

Looking at Structures: A Resource for Learning About PDB Data

Electron density map.

(Click image to enlarge)
Electron density maps are used in determining molecular structure; from "Looking at Structures".
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  online feature 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, visualize structures, read coordinate files, and be aware of 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 Assemblies, Dealing with Coordinates, Methods for Determining Structure, Missing Coordinates and Biological Assemblies, Molecular Graphics Programs, Resolution, R-value and R-free, and Structure Factors and Electron Density.

Looking at Structures is linked from the General Education section of the left-hand menu as Understanding PDB Data

27-Jul-2010

Paper Published

A paper describing dConsensus has been published:

dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment
Kieran Alden, Stella Veretnik, Philip E Bourne
BMC Bioinformatics 2010, 11:310 doi:10.1186/1471-2105-11-310

20-Jul-2010

Upcoming Meeting: ACA

ACA logo.

From July 24-29, the RCSB PDB will be at the 2010 Meeting of the American Crystallographic Association in Chicago, IL.

  • Stop by exhibition booth 108 to meet with members of the RCSB PDB and the PSI Structural Genomics Knowledgebase (PSI SGKB) and pick up many new materials. Learn about new features such as the wwPDB Validation PDFs, the latest version of pdb-extract, the Comparison Tool for sequence and structure, and much more.
  • On Saturday, the Molecule of the Month's David Goodsell will be presenting at the ACA's crystallography education workshop for high school teachers called "Crystallography: World of Wonders".
  • On Sunday, come to the PDB Depositors' Lunch for an update on the wwPDB Common Deposition and Annotation Tool project and to provide your input and feedback. This event will take place at noon in Michigan Room A&B.  Attendees will be asked to sign in and to complete a brief survey. A light lunch will be offered (first come, first served).  
  • A poster describing The wwPDB Common Annotation and Deposition Tool Development will be presented on Monday.
  • The RCSB PDB Poster Prize will be awarded to recognize a student poster presentation involving macromolecular crystallography.

20-Jul-2010

New Release of pdb_extract Available Online and for Download

pdb_extract.

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.

Version V3.10 of pdb_extract has been released, and provides:

  • Support for several new versions of programs (including REFMAC version 5.5 and higher), for a total of 37 programs/packages with hundreds of different formats
  •  Improved extraction and parsing from programs (e.g., PHENIX version 1.4 and later, BUSTER-TNT version 2.8 & higher) and log files (MLPHARE)
  • Support for multiple MTZ file conversion

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

13-Jul-2010

Get the Latest wwPDB News

wwPDB RSS icon

Subscribe to the wwPDB RSS (Really Simple Syndication) Feed to get the latest news as it is published. This feed pushes information to RSS readers so users can easily keep up to date with wwPDB announcements.

The wwPDB News Feed can be accessed by selecting the icon in the top menu bar.

06-Jul-2010

ISMB and 3DSIG Meetings

ISMB 2010
Stop by exhibit booth #24 at the 19th Annual International Conference for Intelligent Systems for Molecular Biology (ISMB) to visit with the RCSB PDB and the PSI SGKB (July 11-13; Boston, MA). 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.

At the 3DSIG satellite meeting on Structural Bioinformatics and Computational Biophysics, Andreas Prlić will present "New RCSB PDB protein comparison tools for sequence and 3D structure" on July 9.  The following day, Phil Bourne will moderate a discussion about the PDB.

06-Jul-2010

Improved Version of ADIT Available

The ADIT deposition tool logo
An updated and enhanced version of ADIT is now available for depositing new entries at http://deposit-beta.rcsb.org/adit/. We encourage depositors to use this new tool and send feedback to deposit@deposit.rcsb.org.

ADIT is used to validate and submit structures to the PDB archive.  Based upon user feedback, we have made improvements to the help statements and documentation provided. This version of ADIT indicates file format errors and provides suggestions for solutions; automatically runs validation checks; and reviews the consistency between sequence and coordinates. The forms for entering sequence information, structure title, author names, and citation information have also been improved.

Currently, this new version of ADIT is being transitioned into production, and will become the default site for deposition on selected days each week for testing. The date of full deployment will depend upon the results of this testing.

Deposition sessions currently in process will not be disrupted; depositors will not have to update any bookmarks or session ID.  

29-Jun-2010

Use Ligand Expo When Depositing Structures with Ligands

The correct stereochemistry of alpha-D-mannose The correct stereochemistry of N-acetyl-D-glucosamine
(Click either 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.

29-Jun-2010

Version 2 NMR Restraint Files Available from the wwPDB FTP

A new set of NMR restraint data files have been added to the wwPDB FTP with this update. These restraint files, identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.

The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen.   NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB;  and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework.  The complexity of this process may have led to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data. More information about the process used to generate these files is available (1-3).

The initial release of the Version 2 NMR restraint files added more than 5700 new files (~310 Mbytes) to the FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.

NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.

Version 1 restraint files will remain in their current directory structure.   Version 2 restraint files are stored in directories named by the middle two characters of the 4-character PDB ID in:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/

These data files are linked symbolically to the single directory:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_restraints_v2/

  1. JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32: 1-12.
  2. WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59: 687-696.
  3. JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45: 389-396. doi: 10.1007/s10858-009-9378-z

22-Jun-2010

Latest Structures Widget

A new widget on the home page displays a slideshow of the latest PDB entries.  

The Latest Structures Widget randomly cycles through all the entries that have been released in the most recent update. It displays the entry title, image, citation and PubMed abstract, if available. Users can pause the slideshow at any point to read the entire abstract, or click on the entry title to view the entry's Structure Summary page. 

More information about the RCSB PDB's home page widgets is available in the most recent issue of the RCSB PDB Newsletter.

15-Jun-2010

Papers published

Articles describing how open access literature is integrated with the RCSB PDB and how scientific illustrators can utilize the PDB data and the RCSB PDB resource have been published:

* Integration of open access literature into the RCSB Protein Data Bank Using BioLit.
Andreas Prlić, Marco A Martinez, Dimitris Dimitropoulos, Bojan Beran, Benjamin T Yukich, Peter W Rose, Philip E Bourne, J Lynn Fink
BMC Bioinformatics (2010) 11:220. doi:10.1186/1471-2105-11-220

* Getting the Most Out of the Protein Data Bank
David S. Goodsell (2009) The Journal of Biocommunication 35: E52-E57.

08-Jun-2010

New Website Features

With this week's update, enhancements have been made to the Structure Comparison Tool, Chemical Component Search, Tabular Reports, the Molecule of the Month, and more. For an overview, see the New Features widget box on the home page or click here.

08-Jun-2010

Improved Version of ADIT Available, Transitional Implementation Starts June 14

An updated and enhanced version of ADIT is now available for depositing new entries at http://deposit-beta.rcsb.org/adit/. We encourage depositors to use this new tool and send feedback to deposit@deposit.rcsb.org.

ADIT is used to validate and submit structures to the PDB archive.  Based upon user feedback, we have made improvements to the help statements and documentation provided. This version of ADIT indicates file format errors and provides suggestions for solutions; automatically runs validation checks; and reviews the consistency between sequence and coordinates. The forms for entering sequence information, structure title, author names, and citation information have also been improved.

Beginning June 14, this new version of ADIT will become the default site for deposition on selected days each week for testing. The date of full deployment will depend upon the results of this testing.

Deposition sessions currently in process will not be disrupted; depositors will not have to update any bookmarks or session ID.

01-Jun-2010

Create a Collage of Structures

Image Collages.

(Click image to enlarge)
This image collage shows some of the structures that were returned for a search of structures that contained the same sequence as chain A of hemoglobin structure 4hhb.

Select 'Custom Report>Image Collage' to display any search result set as a series of tiled molecular pictures. Moving your mouse over each image in the collage displays the structure title; clicking on the small image shows a larger version. The PDB ID listed links to the corresponding Structure Summary page.

Image collages can be customized by the size of the images displayed and how many images are shown per page.

25-May-2010

Search the RCSB PDB in Your Web Browser

In a hurry to search for a PDB entry? Add the RCSB PDB search engine to your web browser to perform queries directly through the browser's search box. "RCSB Full Text or PDB ID Search" and "RCSB Author Search" queries can be performed (alongside similar searches to Google and Yahoo) in the search box of modern browsers such as Firefox (versions 3+) and Internet Explorer (7+).
From Firefox, add RCSB PDB Search options by 
clicking on the arrow.
(Click image to enlarge)
From Firefox, add RCSB PDB Search options by clicking on the arrow.
To add this OpenSearch functionality to your web browser:
  • Visit www.rcsb.org
  • Click on the arrow near the search box
  • For Firefox, select "Add RCSB Full Text or PDB ID Search/Add RCSB Author Search"
  • For IE, select the RCSB PDB search options from the "Add Search Providers" menu
Queries can be performed using this search box 
while browsing any website.
(Click image to enlarge)
Queries can be performed using this search box while browsing any website.
To search the RCSB PDB directly from your browser without going to the RCSB PDB website, select one of the RCSB PDB search engines from the query pulldown menu.  Reading about a PDB entry in a paper? Use the "RCSB Full Text or PDB ID Search" to search by the PDB ID. Use the "RCSB Author Search" to search for structures by the same author. As you type the author name in the browser search box, the "autocomplete" functionality will suggest possible name matches.

18-May-2010

Turn Your Computer into a PDB Structure Kiosk

Kosk Viewer.
Kiosk Viewer Icon.

Highlight structures from your lab, institution, or class with the Molecules in Motion Kiosk Viewer. Using a list of PDB IDs, this full-screen animation program will display any PDB structure from different angles and perspectives. It also focuses on any chemical components within the structure. The Java viewer can be downloaded or launched from the Educational Resources page.

11-May-2010

New Website Features and Widgets

Want to learn about the latest RCSB PDB tools and developments?  The New Features Widget on the home page scrolls through the latest website applications and improvements.  It also links to descriptions of all recent website releases.  Recent items featured in the widget include improved ligand search options, pre-calculated pairwise structure alignments, and enhancements to viewing query results and tabular reports.

The entire home page is comprised of customizable web widgets. Boxes with a dark blue bar on top are widgets that can be moved on the page by dragging the arrow buttons, hidden by selecting "Hide," or included in a customized view.

The green Customize This Page button in the top right corner lets users select which widgets are displayed by default. To only see query-related options, the Molecule of the Month can be replaced with forms to download files and search by sequence.

Other widgets that can be displayed on the home page include the RCSB PDB Comparison Tool for running pairwise structural and sequence alignments, the ADIT Deposition Widget, and the Featured Molecule Widget which displays the RCSB PDB's Molecule of the Month and the Protein Structure Initiative's Featured Molecule.

04-May-2010

wwPDB To Provide Validation Reports as PDFs

As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010 these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.

As these PDB validation reports provide an assessment of structure quality while keeping the coordinate file confidential, we encourage journal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports are already required by the International Union of Crystallography (IUCr) journals as part of their submission process (see Baker et al. (2010) Acta Cryst. F66: 112). The reports are date-stamped, and display the wwPDB processing site logo. They contain essentially the same information, regardless of PDB annotation site. The validation reports will continue to be developed and improved as we receive recommendations from our Validation Task Forces for X-ray, NMR, EM, and small angle scattering methods, and as we further develop our data deposition and processing procedures.

Questions about these reports and the annotation process may be sent to info@wwpdb.org.

04-May-2010

Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive (ftp://ftp.wwpdb.org, ftp://ftp.ebi.ac.uk, and ftp://pdb.protein.osaka-u.ac.jp). These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.

About Version 2 Restraint Files

The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen.

NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB;  and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework.

The complexity of this process may have led to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data.

More information about the process used to generate these files is available (1-3).

Changes to wwPDB FTP Server

The initial release of the Version 2 NMR restraint files will add approximately 5625 new files (310 Mbytes) to the wwPDB FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.

NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.

Version 2 restraint files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/

All of these data files will be symbolically linked to a single directory:

ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_restraints_v2/

Version 1 restraint files will remain in their current directory structure.

For questions, please contact info@wwpdb.org.

References

1. JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12.

2. WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-696.

3. JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389?396.

27-Apr-2010

Newsletter Published

The spring 2010 issue (HTML | PDF) describes new website features and highlights the comprehensive suite of RCSB PDB training materials recently released by OpenHelix. 

In the Education Corner, A Proficiency Rubric for Biomacromolecular 3D Literacy is presented by Robert C. Bateman, Jr. (University of Southern Mississippi) and Paul A. Craig (Rochester Institute of Technology).  This tool can be used to teach and assess student understanding of biomacromolecular concepts.

For printed copies, please send your postal address to info@rcsb.org

20-Apr-2010

Screencasts Demonstrate RCSB PDB Features

Online narrated videos describe how to use ligand searching and website customization tools.

The screencasts currently offered demonstrate:

    * Ligand searching: Using the the MarvinSketch applet  
    * Ligand searching: Advanced MarvinSketch features
    * Ligand searching: Use SMARTS features  
    * Ligand searching: Load a PDB chemical component
    * Customizing Structure Summary pages using Widgets
    * Tour of the left hand menu

Questions about these screencasts or features should be sent to info@rcsb.org.

20-Apr-2010

DNA Day: April 23

DNA Day, April 23 2010.

(Click image to enlarge)
DNA Day, April 23 2010.
DNA Day, which commemorates the completion of the Human Genome Project and the discovery of DNA's double helix, is being celebrated by the National Human Genome Research Institute this year on April 23.  This event encourages teachers and students to celebrate these historic achievements. Related online resources include:

13-Apr-2010

Exhibiting at Experimental Biology (April 24-28)

Rutgers Day 2010.

(Click image to enlarge)
Experimental Biology 2010 .
The RCSB PDB will be exhibiting along with the PSI SGKB at the American Society for Biochemistry and Molecular Biology's Annual Meeting (April 24-28, Anaheim, CA), which is being held in conjunction with the Experimental Biology conference. Stop by booth #93 to meet with RCSB PDB staff, explore new website features, and to pick up the new How Do Drugs Work? poster.

13-Apr-2010

Come build virus models at Rutgers Day (April 24)

Rutgers Day 2010.

(Click image to enlarge)
Rutgers Day.

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 virus structure models next to experiments and demonstrations of how chemistry impacts the food we eat, the air we breathe, the cars we drive, and the medicines we take.

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

06-Apr-2010

Bookmark and Share RCSB PDB Webpages

Share this Page feature.

(Click image to enlarge)
Share this Page feature.

Users can easily send and store URLs using the "Share this Page" button on the upper right side of RCSB PDB webpages.

With this service, favorite PDB entries, Molecule of the Month features, and Looking at Structures pages can be emailed to colleagues or added to link sharing, bookmarking, and social networking sites such as Delicious, Facebook, and Twitter.

30-Mar-2010

Advanced Search: Sequence Motif

The RCSB PDB's Advanced Search lets users build queries of specific types of data. To look for structures with a particular Sequence Motif, try using one of these techniques with the Sequence Features>Sequence Motif option. A Sequence Motif can be an exact sequence or a sequence pattern expressed by regular expression syntax. Regular expressions are powerful notations for defining complex sequence patterns. Click on the sequence to run the example queries:

  •   Short Sequence Fragments

The sequence motif search, unlike BLAST or FASTA, can search for short sequence fragments of any size, such as NPPTP

  •   Wildcard Searches

Use an 'X' in the sequence for wildcard searching.  For example, XPPXP can be entered to look for SH3 domains using the consequence sequence -X-P-P-X-P (where X is a variable residue and P is Proline)

  •   Multiples of Variable Residues

The {n} notation can be used, where n is the number of variable residues. To query a motif with 7 variables between residues W and G, and 20 variable residues between G and L, try WX{7}GX{20}L

  •   Ranges of Variable Residues

The {n,m} notation can be used to indicate ranges of variable residues, where n is the minimum and m the maximum number of repetitions. For example the zinc finger motif that binds Zn in a DNA-binding domain can be expressed as: CX{2,4}CX{12}HX{3,5}H

  •   Motifs at the Beginning of a Sequence

The '^' operator searches for sequence motifs at the beginning of a protein sequence. Two ways of looking for sequences with N-terminal histidine tags are: ^HHHHHH and ^H{6}

  •   Alternative Residues  

Square brackets specify alternative residues at a particular position. To search for a Walker (P loop) motif that binds ATP or GTP, try: [AG]XXXXGK[ST]

The search will look for sequences with A or G, followed by 4 variable residues, then G K, and finally S or T.

Questions about this feature may be sent to info@rcsb.org.


23-Mar-2010

West Windsor Plainsboro High School North Wins New Jersey Science Olympiad Protein Modeling State Finals

West Windsor Plainsboro HS North with their prebuilt model of hemagglutinin.
(Click image to enlarge)
West Windsor Plainsboro HS North with their prebuilt model of hemagglutinin.
Teams had to quickly build a neuraminidase model using Jmol
(Click image to enlarge)
Teams had to quickly build a neuraminidase model using Jmol


At an event that had many impressive and creative models of hemagglutinin and neuraminidase, the team from West Windsor Plainsboro High School North came in first place in protein modeling at the 2010 New Jersey Science Olympiad (NJSO).

At this competitive event, West Windsor-Plainsboro High School South came in second, and New Providence High School came in third out of 24 schools from across the Garden State.

The models were carefully judged by RCSB PDB staff
(Click image to enlarge)
The models were carefully judged by RCSB PDB staff

Teams submitted their hand-built 3D models of a hemagglutinin protein with  an abstract to be judged by staff from the RCSB PDB. Teams enhanced their models with different features to help tell hemagglutinin's story.  At the competition, teams quickly built a model of a selected region of neuraminidase using Jmol and completed a written exam with questions about protein structure and influenza. Teams used the Molecule of the Month and other RCSB PDB resources to help prepare for this event.

Congratulations to all participating teams--there were many great models, abstracts, and responses to the written exam. The final results and a video demonstrating how models are built for this competition are available at education.pdb.org. Questions about the NJ Science Olympiad Protein Modeling trial event should be sent to buildmodels@deposit.rcsb.org.

Special thanks to our judges from the RCSB PDB (Batsal Devkota, Sutapa Ghosh, Christine Zardecki (Event Supervisor) and Jing Zhou), the NJ Science Olympiad organizers, and to the MSOE Center for BioMolecular Modeling for the design of this event.

23-Mar-2010

San Diego Science Festival Expo Day: March 27


Come build virus models at the San Diego Science Festival's (SDSF) Expo Day on Saturday, March 27 at PETCO Park.  

Expo Day is a free, all-day celebration of science with more than 150 hands-on activities and stage shows.  Visitors to the RCSB PDB booth can build 3D virus structure models, watch animations of 3D protein-drug complexes, and take home posters and flyers to learn more.

The San Diego Science Festival is organized by the University of California San Diego, with the support of hundreds of community collaborators, to educate students across the region and inform the public about how important scientific discoveries influence the quality of their daily lives.  Visit http://www.sdsciencefestival.com/ for complete details.

  

16-Mar-2010

Exhibiting at NSTA

The RCSB PDB will be at the National Science Teachers Association's (NSTA) National Conference March 18-21, 2010 in Philadelphia, PA.

NSTA supports science teachers from kindergarten through college.  At exhibit booth 2160, the RCSB PDB will describe how to incorporate protein and nucleic acid structures in their classrooms, demonstrate resources such as the Molecule of the Month, and distribute the How Do Drugs Work poster.

09-Mar-2010

Improved Ligand Searching

Searching for ligands using the RCSB PDB's Advanced Search,  Chemical Structure Search, or top-bar pulldown search has been improved.

The "Chemical Name" search from the top-bar pulldown on every page returns matches to names of small molecules in the wwPDB Chemical Component Dictionary and any synonyms.  Searches by Chemical Name or ID will return structures with matching chemical components that are free ligands or are part of a protein or nucleic acid chain.

In the Advanced Search, searches can be specified to look for free and/or polymeric chemical components.  A "sounds like" option searches for misspelled or incomplete chemical component names.  Advanced Searches using SMILES strings use a similarity (instead of dissimilarity) threshold while specifying polymeric type.

The Chemical Structure Search utilizes the latest version of the ChemAxon MarvinSketch applet (5.3.0.1).  Tutorials and screencasts are available to help explore these features.

A detailed description with examples of these new features is available.

For an overview of all recently-added features, see the New Features widget box on the home page or click here.

02-Mar-2010

New Website Features

The latest website release includes many new features, including a fully customizable home page, improved ligand search options, pre-calculated pairwise structure alignments, enhancements to viewing query results and tabular reports, and much more. For an overview of all of these features, see the New Features widget box on the home page or click here.


23-Feb-2010

Online Narrated Tutorial Demonstrates How to Use the RCSB PDB

Comprehensive training materials to introduce users to the features and functionality of the RCSB PDB are now freely available at openhelix.com.

The new training tools include an online narrated tutorial that demonstrates basic and advanced searches, how to generate reports, the different options for exploring individual structures, and many of the resources and tools available at the RCSB PDB for research and education. The full tutorial runs for about an hour, and can be navigated by specific chapters.

The animated PowerPoint slides used as a basis for the tutorial can be downloaded, along with slide handouts, and exercises. These materials are freely available for teachers and professors to create classroom content.

OpenHelix has also created Quick Reference Cards for the RCSB PDB that highlight search strategies, features and functionality. The cards can be ordered at www.openhelix.com at no cost; shipping is free within the United States. 

23-Feb-2010

Changes to the wwPDB Policy for Depositing Polypeptide Structures

The wwPDB now accepts polypeptide structure depositions of all gene products; all naturally-occuring, non-ribosomally synthesized peptides, such as antibiotics; and all peptidic repeat units of larger polymers, such as fibrous and amyloid polymers. In addition, non-naturally occurring synthetic peptides with at least 24 residues will be accepted for deposition.

16-Feb-2010

Exhibition at the Biophysical Society Meeting

The RCSB PDB will be exhibiting along with the PSI SGKB at the 54th Annual Meeting of the Biophysical Society (February 20 - 24) in San Francisco, CA. Stop by booth #227 to meet with RCSB PDB staff and to pick up the new How Do Drugs Work? poster. On Monday, February 22, How to use the PSI Structural Genomics Knowledgebase to Enable Research will be presented at poster board B102.

Education and Outreach at the RCSB Protein Data Bank will be part of the poster session on Wednesday, February 24.

09-Feb-2010

Poster Download: How Do Drugs Work?

New Poster: How do drugs work.

New poster: How Do Drugs Work?

A new poster that explores different kinds of protein-drug structures found in the PDB archive is available for download as a poster (26 x 38", low res 1MB, high res 11 MB) and flyer (8 1/2 x 11", 3 MB).

How Do Drugs Work? was inspired by the success and enduring popularity of 2002's poster on Molecular Machinery: A Tour of the Protein Data Bank.

Written and illustrated in a style similar to the Molecule of the Month series, the poster uses PDB structures to discuss antibiotics and antivirals, chemotherapy, drug metabolism, drugs of signaling proteins, and lifestyle drugs.

The How Do Drugs Work? poster and flyer can be downloaded from the RCSB PDB's Educational Resources page. Printed copies will be distributed at scientific and educational meetings.

02-Feb-2010

Newsletter Published

The winter 2010 issue (HTML | PDF) highlights 2009 deposition, release, and access statistics, describes new website features for searching and reporting, and reviews recent outreach activities. In the Education Corner, IJsbrand M. Kramer discusses the benefits of using more "realistic" molecular images in university cell biology courses.

For printed copies, please send your postal address to info@rcsb.org.

02-Feb-2010

wwPDB FTP Advisory Notice

The PDB archive can be accessed at FTP sites at the RCSB PDB, PDBe, and PDBj. The update schedules for these sites have been coordinated to be simultaneous. All updates now occur at the target time of Wednesday 00:00 UTC (Coordinated Universal Time).

Currently, the release date reflected in the initial REVDAT record in a PDB file is marked as a Tuesday date. This release date will be changed to mirror the Wednesday release as of March 31, 2010. The file's timestamp of the Friday before release will not be changed.

26-Jan-2010

Comparison Tool for Exploring Sequence and Structure Alignments

4HHB.A vs 4HHB.B using jCE.

(Click image to enlarge)
4HHB.A vs 4HHB.B using jCE (click to launch).

The Comparison Tool calculates pairwise sequence and structure alignments using different methods. This feature is available on the Compare Structures web page and as a downloadable web widget.

The current sequence alignments possible are blast2seq, Needleman-Wunsch, and Smith-Waterman. Structure alignments can be performed using FATCAT and CE through a Java applet launched from the RCSB PDB site. Mammoth, TM-Align, and TopMatch structure alignments will be launched at their related external sites.

This functionality is also integrated with the Sequence Clusters offered from each entry's Sequence Similarity tab. Users can select a pair of chains from a given sequence cluster, and then run either sequence or structure alignments. For example, the Sequence Similarity tab for entry 4hhb offers sequence clusters at different similarity cutoffs.  Users can select a pair of chains from a given sequence cluster (95% for this example), and then run the sequence or structure alignments available from the Comparison Tool.  


19-Jan-2010

NJ Science Olympiad Protein Modeling Results

Students built their models using Jmol and Mini-Toobers
(Click image to enlarge)
Students built their models using Jmol and Mini-Toobers
After the competitions, RCSB PDB annotators gave feedback about the models
(Click image to enlarge)
After the competitions, RCSB PDB annotators gave feedback about the models

35 teams across New Jersey expressed their knowledge about hemagglutinin and protein structure at the Science Olympiad. The RCSB PDB sponsored the protein modeling trial event at the three regional competitions. Teams were judged on their knowledge of protein structure and function based upon a protein model built before the competition, a model quickly built at the competition, and a written exam. The top scoring teams were:

Cherry Hill High School East's Akshay Subramaniam and Tony Chen came in first place at the southern regional.
(Click image to enlarge)
Cherry Hill High School East's Akshay Subramaniam and Tony Chen came in first place at the southern regional.


    Southern Regional (January 9, Camden County College)
  1. Cherry Hill High School East (80.50)
  2. MATES Academy (74.80)
  3. The Lawrencevile School (71.00)


    Central Regional (January 12, Union County College)
  1. South Brunswick (87.00)
  2. Westfield (86.50)
  3. Hillsborough (76.50)


    Northern Regional (January 14, New Jersey Institute of Technology)
  1. West Windsor Plainsboro South (96.50)
  2. Livingston (89.50)
  3. Princeton (79.50)

Information and resources about this event are posted at education.pdb.org and on @buildmodels.

Special thanks to our judges from the RCSB PDB (Batsal Devkota, Sutapa Ghosh, Monica Sekharan, Chengua Shao, Huangwang Yang, Christine Zardecki, Jing Zhou, and Marina Zhuravleva), 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 finals in March!


 

12-Jan-2010

Time-stamped Copies of PDB Archive Available via FTP

A snapshot of the PDB archive (ftp.wwpdb.org) as of January 4, 2010 has been added to ftp://snapshots.wwpdb.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 directory 20100104 includes the 62,388 experimentally-determined coordinate files and related experimental data that were available at that time. 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.

The script at ftp://snapshots.wwpdb.org/rsyncSnapshots.sh may be used to make a local copy of a snapshot or sections of the snapshot..

05-Jan-2010

2009 Annual Report Published

The 2009 Annual Report (PDF) highlights recent accomplishments and explores the RCSB PDB's different activities in data deposition, query, and education. This publication is distributed to the diverse community of PDB users in academia, industry, and education. If you would like a printed copy, please send your postal address to info@rcsb.org.