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Year 2013 News

Contents:

31-Dec-2013 Happy International Year of Crystallography
24-Dec-2013 Annual Report Published
17-Dec-2013 Paper Published
10-Dec-2013 Quick Tour of Search Results
03-Dec-2013 World AIDS Day Symposium
26-Nov-2013 Browse Membrane Transport Proteins
19-Nov-2013 Help Desk Questions and Answers
12-Nov-2013 Upcoming Meeting: ABRCMS
05-Nov-2013 Comparison Tool for Exploring Sequence and Structure Alignments
29-Oct-2013 Find Structures Using the Protein Symmetry Browser
22-Oct-2013 Fall Newsletter Published
15-Oct-2013 Search by Gene Name
08-Oct-2013 Find Drugs in the PDB
08-Oct-2013 Retirement of SOAP Services
01-Oct-2013 New PDB-101 Animation
24-Sep-2013 wwPDB Public Symposium
24-Sep-2013 Workshop on Theoretical Model Validation and PDBx/mmCIF Data Exchange Format
24-Sep-2013 Beta #11 of the RCSB PDB Mobile Android App is Available
17-Sep-2013 Improved Searching with New Sequence Identity Cutoff
17-Sep-2013 wwPDB Public Symposium
10-Sep-2013 New Website Release
10-Sep-2013 Poster Prize Awarded at ECM
03-Sep-2013 Head Back to School with PDB-101
27-Aug-2013 Map PDB Structures to Full-length Protein Sequences
20-Aug-2013 Poster Prize Awarded at ISGO
20-Aug-2013 Explore Gallery View of Search Results
20-Aug-2013 Join the RCSB PDB Team
13-Aug-2013 NOTICE: RCSB PDB Deposition Service Interruption
13-Aug-2013 Poster Prize Awarded at ACA, ISMB
06-Aug-2013 Ligand Reports
30-Jul-2013 Smart Searching with the Top Bar Suggestion Box
23-Jul-2013 Upcoming Meeting: ICSG2013-SLS
23-Jul-2013 Join the RCSB PDB Team
23-Jul-2013 Beta version #4 of RCSB PDB Mobile for Android
16-Jul-2013 Upcoming Meetings: ACA & ISMB/ECCB
09-Jul-2013 Spring Newsletter Published
09-Jul-2013 Beta version #3 of RCSB PDB Mobile for Android
02-Jul-2013 Build 3D Paper Models at PDB-101
25-Jun-2013 Keep Up-to-Date with the RCSB PDB
18-Jun-2013 Create High Resolution Images
11-Jun-2013 Search the PDB Using Drill-down Pie Charts
11-Jun-2013 New Paper: Trendspotting in the PDB
04-Jun-2013 Map PDB Structures to Full-length Protein Sequences
28-May-2013 Browse the Anatomical Therapeutic Chemical Classification System to Find Structures
21-May-2013 Web Services for Accessing PDB Data
14-May-2013 Personalize the RCSB PDB
07-May-2013 New PDB-101 Features
30-Apr-2013 Updated Version of MAXIT Available
23-Apr-2013 Rutgers Day (April 27)
23-Apr-2013 DNA Day 2013: April 25
23-Apr-2013 Beta Test RCSB PDB Mobile for Android
16-Apr-2013 Upcoming Meeting: Experimental Biology and ASBMB
09-Apr-2013 Visit the RCSB PDB at NSTA
09-Apr-2013 Spring Newsletter Published
02-Apr-2013 Search, View Annotations, and Visualize Peptide-like Antibiotic and Inhibitor Molecules
26-Mar-2013 3D Visualization of Protein Symmetry
19-Mar-2013 Visit the San Diego Festival of Science and Engineering on March 23
19-Mar-2013 Distribution of PDB Data by Protein Stoichiometry and Symmetry
12-Mar-2013 Access Drugs and Drug Targets in the PDB
05-Mar-2013 New Website Release
26-Feb-2013 Browse the PDB by GO Terms, EC Number, Source Organism, and More
19-Feb-2013 Build complex queries with Advanced Search
12-Feb-2013 Poster Prize Awarded at AsCA
05-Feb-2013 Author Profiles: Timeline Display of a Researcher's Structures
05-Feb-2013 News Reader Survey
29-Jan-2013 Visit the Biomolecular Discovery Dome at Biophysical Society
29-Jan-2013 Join the RCSB PDB Team
22-Jan-2013 Portable Molecules (of the Month)
22-Jan-2013 Revision History Widget
15-Jan-2013 Quick Tour of Search Results
08-Jan-2013 Winter Newsletter Published
08-Jan-2013 News Reader Survey
01-Jan-2013 Annual Report Published

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


31-Dec-2013

Happy International Year of Crystallography

In celebration of IYCr, the wwPDB has created a 2014 calendar that illustrates how X-ray crystallography enables our understanding of biology at the atomic level. Each month illustrates milestone crystal structures in the PDB archive. The calendar can be downloaded as a PDF, individual images, a PowerPoint presentation, and desktop wallpaper from wwpdb.org. The wwPDB will also host different IYCr-related events throughout the year.

Celebration of IYCr

24-Dec-2013

Annual Report Published

Download the 2013 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

The recently published Annual Report highlights the RCSB PDB's accomplishments for 2013. It also reviews topics ranging from deposition statistics to the new Protein Feature View to the results from a recent user survey.

wwPDB efforts, including the development of the Common Deposition and Annotation Tool, are also highlighted.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive. This edition, the RCSB PDB's fourteenth, is available as a PDF download. If you would like a printed copy, please send your postal address to info@rcsb.org.

Annual Report Full News

The 2013 Annual Report cover displays a representation of the HIV virus surrounded by examples of related protein-drug complexes. These include rilpivirne bound to HIV-1 reverse transcriptase (PDB ID 4g1q); dolutegravir bound to the PFV virus, a protein similar to HIV integrase (PDB ID 3s3m); and darunavir bound to HIV protease (PDB ID 4hla). Molecular snapshots like these help researchers discover and develop drugs for the fight against HIV.

17-Dec-2013

Paper Published

A new paper has been published that describes the module used to process chemical components in deposited PDB entries as part of the new wwPDB Common Deposition and Annotation System:

J.Y. Young, Z. Feng, D. Dimitropoulos, R. Sala, J. Westbrook, M. Zhuravleva, C. Shao, M. Quesada, E. Peisach, H.M. Berman. (2013) Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database 2013: bat079.

This new system is currently in testing. For more information, see wwpdb.org.

10-Dec-2013

Quick Tour of Search Results

View this video to see the different options available for exploring search results.

03-Dec-2013

World AIDS Day Symposium

On December 7, 2013, Rutgers will host presentations from clinicians, scientists, and patients about HIV/AIDS.

Today HIV/AIDS is a treatable chronic illness. Come to this symposium to learn from leading clinicians and scientists about the history of HIV/AIDS, its clinical management and the science that has led to the design of specific anti-HIV drugs. Learn about the molecular basis for why patients develop resistance to anti-HIV drugs and the challenges in the quest for an HIV vaccine. Listen to patient panel discussions to learn about what it means to be living with HIV.

This event is sponsored by the Rutgers Childrens AIDS Network, RCSB Protein Data Bank, and the Robert Wood Johnson AIDS Program. Registration is free but required. To register email sdutta2@rcsb.rutgers.edu and provide the names of all attendees. 

Flyer World AIDS Day Symposium

26-Nov-2013

Browse Membrane Transport Proteins

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.

ALT_TEXT

Selected structures found from a TC search for 1.G: Viral Fusion Pores.
Use the Transporter Classification Browser to find PDB's 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.

19-Nov-2013

Help Desk Questions and Answers

The RCSB PDB Help Desk supports people from all over the world who write daily for assistance with the website, archive and general structural biology. About 1000 electronic conversations are initiated by nearly as many unique users in any given year. Questions come from students new to structural biology, users interested in the general study of science, and domain experts from various disciplines that utilize PDB data.

Types of questions to the help desk (from the 2012 RCSB PDB Annual Report)

Types of questions to the help desk (from the 2012 RCSB PDB Annual Report)


Many of these conversations lead to new developments and enhancements to the website and services offered.

Frequently asked questions include:

Q: Can I use this figure in my lecture/thesis/book?
A: All images, including Molecule of the Month illustrations, can be reprinted. Citation and full usage information is listed online.

Q: Is there a Web Service that will return entity descriptions?
A: Access to entity descriptions are one of the RESTful (REpresentational State Transfer) Web Services offered to make accessing data easier. A full list of available services is available; please let us know if there are other services that you would like to use.

Q: What is a PDB chain?
A: The term "chain" refers to a protein or nucleic acid macromolecule. A PDB entry may have multiple copies of the same "chain." For example, hemoglobin entry 4hhb contains 4 protein chains: 2 copies of the alpha chain and 2 copies of the beta chain. See PDB-101’s Understanding PDB Data for more.

Q: How do structures on hold for publication get released?
A: The wwPDB aims to release entries as close to the publication date as possible. With some entries, journals provide advance publication notice, and for others, citation information is sent by the structure authors or other users. Software is also regularly used to search for matches in PubMed. Have a citation? Please send it to the help desk.

Want to learn more? Read The Ins and Outs of the RCSB PDB Help Desk: What do we learn from our users? What do they learn from us? by Rachel Kramer Green from the Spring 2013 Newsletter.

12-Nov-2013

Upcoming Meeting: ABRCMS

The next RCSB PDB event will be at the Annual Biomedical Research Conference for Minority Students (November 13-16; Nashville, TN). Visit booth 715 for website demonstrations and related free materials.

ABRCMS

Visit the RCSB PDB in booth 715

Signed copies of The Machinery of Life (by Molecule of the Month author David Goodsell) will be raffled off in the exhibition hall.



The Machinery of Life was recently highlighted in a commercial that can be viewed online.

05-Nov-2013

Comparison Tool for Exploring Sequence and Structure Alignments

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, TM-Align, TopMatch, Dali).

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) and circular permutations that are difficult for many alignment algorithms to detect (via jCE).

The Comparison Tool 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 (with similarity cutoffs of 100%, 95%, 90%, 70%, 50%, 40%, or 30%) and run alignment comparisons.

Documentation and acknowledgements are available from the Compare Structures page.

Comparison Tool

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

29-Oct-2013

Find Structures Using the Protein Symmetry Browser

RCSB PDB's Browse Database feature explores the PDB archive using different hierarchical trees. An option to browse structures based on protein symmetry has been added.

Select the Protein Symmetry tab from the Browse Database interface to navigate through the global and local symmetry and pseudosymmetry hierarchy, view the number of associated PDB structures, and access the related entries.

The browser opens up the top level in the hierarchy. Clicking on the arrow/folder icons expands the respective nodes. Clicking on the name of the node will retrieve all PDB entries associated with that type of symmetry.

Protein symmetry is calculated for all protein complexes in the PDB, and updated weekly. A detailed description of protein symmetry in the PDB is available.

Other Browse options include GO Terms, Enzyme Classification, Transporter Classification, Source Organism, Genome Location, MeSH terms, SCOP, CATH, ATC, and Transporter Classification.



Use the Protein Symmetry Browser to find PDB structures

22-Oct-2013

Fall Newsletter Published

The Fall 2013 issue of the RCSB PDB Newsletter is now available.

This newsletter describes the recent wwPDB Symposium: A Celebration of Open Access in Structural Biology, recent deposition and website statistics, and an update on the new wwPDB Deposition & Annotation System.

Recent features added to the main RCSB PDB website and to PDB-101 are also highlighted.

The Education Corner hosts In Touch with Molecules: Improving student learning with innovative molecular models by Jodi Davenport, Matt Silberglitt (WestEd), and  Arthur Olson (The Scripps Research Institute).

Starting with this issue, the newsletter will only be published online. We encourage all of our readers to sign up for quarterly newsletter electronic updates.

Past issues of the newsletter are available online.

15-Oct-2013

Search by Gene Name

A gene name option is available from the simple search bar at the top of RCSB PDB pages.
To begin, start typing the name of a gene (for example brca) and a list of possible suggestions will appear.



Then, select one of the suggestions in the "UniProt Gene Name" category.  This will return a corresponding Protein Feature View page.



Among other things, the Protein Feature View page provides a graphical summary of a full-length protein sequence from UniProt and how it relates to PDB entries.

The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

08-Oct-2013

Find Drugs in the PDB

Two new tables provide access to drug and drug target information from DrugBank that are mapped to PDB entries with each weekly update. These tables, accessed from the Tools menu, can be searched by generic or brand drug name, filtered, and sorted.

The Drugs Bound to Primary Targets Table lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.

Thumbnail of Drugs to PDB ID mapping page

The Primary Drug Targets Table lists primary drug targets in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands). Biotherapeutics, such as complexes with monoclonal antibodies, are included

Drug Target Only

A detailed description of the Drug and Drug Target Mapping page is available.



08-Oct-2013

Retirement of SOAP Services

Effective early December 2013, RCSB PDB SOAP Web Services will be retired. Developers still using SOAP services are asked to transition to the equivalent and easier to use RESTful Web Services.

The RESTful API offers:

  • Generic query to execute any search available on the website as a web service call.
  • Custom report service which offers a flexible way to return data in CSV, Excel, and XML format.
  • Several specialized services to retrieve information about the status and description of PDB entries, chemical components, and sequence-based mappings.

Please contact us for any assistance with the transition from SOAP to RESTful.



01-Oct-2013

New PDB-101 Animation

Visit PDB-101 to learn about the 3D shape and function of macromolecules.  This video What is a Protein? illustrates the path from primary to quaternary structure. It is also a PDF flyer available for download.





24-Sep-2013

wwPDB Public Symposium

wwPDB Symposium

Recognizing the career and achievements of Professor Helen M. Berman

A special public symposium A Celebration of Open Access in Structural Biology: Recognizing the career and achievements of Professor Helen M. Berman will be held September 26, 2013 at Rutgers, The State University of New Jersey.

The list of speakers and sponsors is available at http://www.wwpdb.org/outreach2013.html

24-Sep-2013

Workshop on Theoretical Model Validation and PDBx/mmCIF Data Exchange Format

Rutgers will host the Model Validation Working Group Meeting and a Workshop on the PDBx/mmCIF Data Exchange Format for Structural Biology in October 2013.  Details for both events are available from the Protein Model Portal

24-Sep-2013

Beta #11 of the RCSB PDB Mobile Android App is Available

Beta version #11 of RCSB PDB <i>Mobile</i> for Android

(Click image to enlarge)
Beta version #11 of RCSB PDB Mobile for Android

(PLEASE NOTE: if you have a previous beta version of the software installed, you must manually uninstall it first via Android settings -> Apps)

Beta #11 of the Android version of RCSB PDB Mobile app is available for download. This will likely be the final beta release before the app becomes available in the Google Play store. Please note the app requirements below, which have changed:

  • The app will only be supported on Android version 4.0 or above, though it may be installed on earlier versions of Android above 2.3.3
  • 35mb storage is required to install the app, and a further 60mb of storage (i.e. SD card or other storage) is required to store the app's internal index
  • This release of the app does not support tablet devices; that support will be implemented in a future update

RCSB PDB Mobile is also available the iPhone/iPod/iPad from the Apple App Store.

17-Sep-2013

Improved Searching with New Sequence Identity Cutoff

A sequence identity cutoff value option has been added to Advanced Search for "Sequence (BLAST/FASTA/PSI-BLAST)". 


To use this feature, enter a sequence by typing a PDB ID in the Structure ID text box and selecting a Chain ID from the pull-down menu or by pasting a sequence into the Sequence text box.


Using the Sequence Identity Cutoff (a percentage value between 0 and 100) option, the results returned will have at least the specified sequence identity to the target sequence. For example, entering 100% returns entries with exactly match the same sequence.  As many structures have low E-values but only a few have high sequence identity with the target sequence, fewer results will be returned when using this feature. 


The % sequence identity can be seen by displaying the sequence alignment on the query results page.  All results returned will have sequence identity greater than or equal to the cutoff used.

This Sequence Identity Cutoff differs from the 'retrieve representatives' option found at the bottom of the Advanced Search screen and on the Query Results pages.  The option to "retrieve only representatives at XX% sequence identity utilizes RCSB PDB's use of BLAST clustering to remove redundant sequences, and returns one representative per cluster.

Advance Search Interface Advance Search Interface



17-Sep-2013

wwPDB Public Symposium

wwPDB Symposium

Recognizing the career and achievements of Professor Helen M. Berman

A special public symposium A Celebration of Open Access in Structural Biology: Recognizing the career and achievements of Professor Helen M. Berman will be held September 26, 2013 at Rutgers, The State University of New Jersey.

The list of speakers and sponsors is available at http://www.wwpdb.org/outreach2013.html

10-Sep-2013

New Website Release

The new Protein Symmetry Browser
The new Protein Symmetry Browser

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

Drug and Drug Target Mapping. Two new tables provide access to drug and drug target information from DrugBank mapped to PDB entries. These tables, accessed from the Tools menu, can be searched by generic or brand drug name, filtered, and sorted:

  • The Drugs Bound to Primary Targets Table lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.
  • The Primary Drug Targets Table lists primary drug targets in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands).  Biotherapeutics, such as complexes with monoclonal antibodies, are included.

Protein Symmetry. Options to explore local and helical symmetry have been added to our protein symmetry resources, which include data distribution summaries (on the home page and for search results), Advanced Search, and the Jmol viewer.

The new Protein Symmetry Browser can also be used to browse for structures.

New Jmol/3D View pageThe layout of options for viewing a structure in 3D has been improved to provide quick access.  Select from views that highlight Secondary Structure, Subunits, or Symmetry, or use the Custom View to utilize different features.  All views can be saved as an image file.

See the What's New page for more new features and examples.

10-Sep-2013

Poster Prize Awarded at ECM

Jonathan C. Brooks-Bartlett

Jonathan C. Brooks-Bartlett

At the 28th European Crystallography Meeting (August 25-29, Warwick, UK), the RCSB PDB Poster Prize was awarded to Jonathan C. Brooks-Bartlett  for Exploring the Relationships Between Diffracted Intensity Decay and a New Dose Metric for MX (Jonathan C. Brooks-Bartlett, Oliver B. Zeldin, Elspeth F. Garman; Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford).

Many thanks to judges and organizers: Alessia Bacchi (University of Parma), Ralf Ficner (University of G¯öttingen), Dean Keeble (University of Warwick), Pietro Roversi (University of Oxford), and Marjolein Thunnissen (Lund University).

All 2013 awardees are listed on the RCSB PDB website and will receive an educational book.

03-Sep-2013

Head Back to School with PDB-101

The DNA paper model and <i>Molecule of the Month</i> article have been translated into Spanish.
The DNA paper model and Molecule of the Month article have been translated into Spanish.

PDB-101 resources promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.  A video tour highlights some of the different features available.

Recent additions to PDB-101's Educational Resources include:

The flyer What is a Protein? introduces protein structure and function to beginners (PDF).

Structures of the Citric Acid Cycle illustrates the PDB structures involved in this important metabolic pathway (PDF).

A new page groups together 3D paper models available for download.

This includes a video demontration of the DNA model, DNA resources translated into Spanish, and the HIV capsid model (PDF).

To visit PDB-101 from the main RCSB PDB site, click on the blackboard PDB-101 logo or its related widget in the left-hand menu. This view offers easy navigation: select any Molecule of the Month article from the top bar pull-down menu or choose one of the tabs to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website.

27-Aug-2013

Map PDB Structures to Full-length Protein Sequences

Protein Feature View from 2VX3's Structure Summary page.

(Click image to enlarge)
Protein Feature View from 2VX3's Structure Summary page.
Protein Feature View for all entries with UniProtKB ID Q13627. This image can be exported as an SVG file.

(Click image to enlarge)
Protein Feature View for all entries with UniProtKB ID Q13627. This image can be exported as an SVG file.

The new Protein Feature View visually summarizes how a full-length protein sequence from UniProtKB corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are also displayed.

For individual entries, the Protein Feature View is available from the Molecular Description Widget on Structure Summary pages.  The example shown for PDB ID 2VX3 illustrates how the ranges of a protein that have been observed in an experiment (in blue) correspond to the full length UniProtKB sequence (in grey). The secondary structure information from the PDB entry is also shown (helices in red, beta strands in yellow).

Various features that are known for the UniProtKB sequence are displayed in green as they correlate with regions in the PDB entry. Active sites (from UniProtKB and the PDB entry) are also annotated. Moving the mouse cursor over the 'lollipops' displays the residue label. Mousing over the images shown in the "Secstruc" row reveals secondary
structure from the PDB entry.

This view can be expanded to map all PDB entries related to a single UniProtKB sequence by selecting the Protein Feature View link shown in this widget. By default, a few representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available.  Selecting the plus sign or the "Show All" button will expand this view to show all related PDB chains, which can then be sorted by resolution, length, and release date.  These Protein View images can be exported as Scalable Vector Graphics (SVG) files. 

The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

20-Aug-2013

Poster Prize Awarded at ISGO

Youngchang Kim

Youngchang Kim

At the International Conference on Structural Genomics (July 29-August 1, Sapporo, Japan), the RCSB PDB Poster Prize was awarded to Youngchang Kim for Structural Analysis of the Catalytic Mechanism of NDM-1 (Youngchang Kim,1 Mark Cunningham,2 Christine Tesar,1 Robert Jedrzejczak,1 Joseph Mire,2 Andrew Binkowski,1 Gyorgy Babnigg,1 James Sacchettini,3 Andrzej Joachimiak;1 1Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL, 2Physics and Geology, The University of Texas-Pan American, Edinburg, TX,  3Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX).

Many thanks to judges Stephen Burley (RCSB PDB), Katsumi Maenaka (Hokkaido University), and Tom Terwilliger (Los Alamos National Laboratory).

All 2013 awardees will be listed on the RCSB PDB website and will receive an educational book.

20-Aug-2013

Explore Gallery View of Search Results

Gallery view for a search for structures with tetrahedral symmetry. Images can be resized, and entries can be selected or deselected.

(Click image to enlarge)
Gallery view for a search for structures with tetrahedral symmetry. Images can be resized, and entries can be selected or deselected.

Query results can be browsed using detailed, condensed, timeline or gallery views. These views are synchronized; selecting or deselecting a structure in one view will have the same effect in the others.

To view only the images of structures that match a given search, select View>Gallery from the option offered. 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; the PDB IDs can also be hidden from the gallery.

20-Aug-2013

Join the RCSB PDB Team

Come code with us.

(Click image to enlarge)
Come code with us.

RCSB (Rutgers) is looking for a Senior Web Application Developer

13-Aug-2013

NOTICE: RCSB PDB Deposition Service Interruption

On Tuesday, August 20, 2013, RCSB PDB deposition services (ADIT, Validation Server, pdb-extract, Ligand Expo) and annotation staff email will be down as Rutgers University upgrades the campus power system.  The outage is scheduled to begin at 6:00 a.m. Eastern Time and end early morning on August 21.  

NO NEED TO HOLD OFF ON DEPOSITIONS!  During this period, depositors can take advantage of wwPDB partner relationships and submit new entries with PDBe and PDBj. RCSB PDB 'in progress' depositions will not be accessible during this time.

The RCSB PDB query website (rcsb.org) and help desk (info@rcsb.org) will not be affected.



13-Aug-2013

Poster Prize Awarded at ACA, ISMB

Matthias Dietzen

Matthias Dietzen
Peter Lee

Peter Lee

The RCSB PDB Poster Prize was recently awarded at the ACA and ISMB meetings.

At the American Crystallographic Association's Annual Meeting (July 20-24; Honolulu, HI), the award went to Peter Lee for Head Hunting: Targeting the Influenza Hemagglutinin Receptor Binding Site (Peter S. Lee,1 Ayato Takada,2 James E. Crowe Jr.,3  Yoshikazu Kurosawa,4 Ian A. Wilson;1 1The Scripps Research Institute, 2Hokkaido University, 3Vanderbilt University, 4Fujita Health University). Many thanks to judges Champion Deivanayagam (University of Alabama at Birminham), Robert McKenna (University of Florida), and Clyde Smith (Stanford University); and to Marcia Colquhoun and the ACA.

At the International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (July 21-23, Berlin, Germany), the award went to Matthias Dietzen for Three-Dimensional Modeling of Macromolecular Assemblies by Efficient Combination of Pairwise Dockings (Matthias Dietzen,1 Olga Kalinina,1 Katerina Taškova,2 Benny Kneissl,3 Elmar Jaenicke,3 Heinz Decker,3 Thomas Lengauer,1 Andreas Hildebrandt;3 1Max Planck Institute for Informatics, Saarbr¯ücken, Germany, 2Intel Visual Computing Institute, Saarbr¯ücken, Germany, 3Johannes Gutenberg University, Mainz, Germany)

Many thanks to the Steven Leard, the International Society for Computational Biology, and the judges: Yana Bromberg (Chair, Rutgers), Manuel Corpas (Independent), Jeroen de Ridder (Delft University of Technology), Nils Gehlenborg (Harvard), Tatyana Goldberg (TU Munich), Edda Kloppmann (TU Munich), Geoff Macintyre (University of Melbourne), Magali Michaut (Netherlands Cancer Institute), Nikolay Samusik (Stanford), Venkata P. Satagopam (EMBL), Oren Tzfadia (Weizmann Institute of Science).

All 2013 awardees will be listed on the RCSB PDB website and will receive an educational book.


06-Aug-2013

Ligand Reports

Ligand Summary Reports include information about chemical components associated with the entries in a results set, such as formula, molecular weight, name, SMILES string, which PDB entries are related to the ligand, and whether the chemical component is included as a free ligand or as part of the polymer chain.


Ligand Hits
To generate a report, select the Ligand Hits tab for any set of query results.


Generate Reports The Generate Reports options available for Ligand Hits includes a collage of ligand images, or the Ligand Summary Report.


Summary Report
Click on the triangle to reveal the sub-table of PDB IDs.

The Ligand Summary Report lists formula, molecular weight, name, SMILES string, which PDB entries are related to the ligand, and how they are related.

For each ligand, a sub-table can be selected to list all related PDB entries that contain the ligand, the entries that contain the ligand as a free ligand, and entries that contain the ligand as part of a larger, polymeric ligand.

To display this sub-table, select the triangle shown next to the Ligand ID. The display is limited to 15 PDB IDs in each column. For ligands associated with more than 15 PDB entries, the ... [more] link will launch a query for that set of structures.


All tabular report features are also available, including sorting, filtering, export to other report formats, and column customization.



30-Jul-2013

Smart Searching with the Top Bar Suggestion Box

Simple text searches complement other RCSB PDB tools: the Explore Archive widget, Browse Database, and Advanced Search.

(Click image to enlarge)
Simple text searches complement other RCSB PDB tools: the Explore Archive widget, Browse Database, and Advanced Search.

The top search bar helps users easily and intuitively create simple text searches. It recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.  

Typing text in the top search bar launches an interactive pop-up box that suggests possible matches that are organized by categories ranging from author name to ontology terms.

For example, autosuggestions for the input "bird" will organize structures with authors whose names contain "bird" and structures from the organism bird by category.  Users who want to perform a simple, non-categorized text search can click the magnifying glass icon or press return.  Entering SMILES strings will suggest options to perform substructure, exact structure, or similar chemical structure searches, while typing in a sequence will offer different BLAST search options.

The top menu bar recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.

The top menu bar recognizes particular types of syntax, such as SMILES strings and sequences, and suggests related search options accordingly.


The top search can be also be limited to quick searches on Author, Macromolecule name, Sequence, or Ligand by selecting the related title from above the text box. 

Simple text searches complement other RCSB PDB tools: the Explore Archive widget provides browsable data distribution summaries, Browse Database explores the PDB archive using different hierarchical trees, and Advanced Search combines multiple searches of specific types of data.

23-Jul-2013

Upcoming Meeting: ICSG2013-SLS

ICSG

At the Structural Life Science/Seventh International Conference on Structural Genomics (July 29-August 1; Sapporo, Japan), Stephen Burley (Associate Director, RCSB PDB) will present wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information.

PDBj Director Haruki Nakamura and Stephen Burley will present a poster on The New wwPDB Deposition and Annotation System.

The RCSB PDB Poster Prize will be awarded for most creative use of the PDB.

23-Jul-2013

Join the RCSB PDB Team

Join the RCSB PDB Annotation Team.

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Join the RCSB PDB Annotation Team.

The RCSB PDB is looking for a  Biochemical Information & Annotation Specialist

23-Jul-2013

Beta version #4 of RCSB PDB Mobile for Android

Beta version #4 of RCSB PDB <i>Mobile</i> for Android

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Beta version #4 of RCSB PDB Mobile for Android

(PLEASE NOTE: if you have a previous beta version of the software installed, you must manually uninstall it first via Android settings -> Apps)

Beta #4 of the Android version of RCSB PDB Mobile app is available for download. This update includes fixes for some bugs.

RCSB PDB users with Android phones or tablets using version 2.3 or higher of the Android OS satisfying the testing requirements can download beta version #4 of RCSB PDB Mobile. Please note that tablet support is currently preliminary and will be firmed up in a future beta release.

This edition of RCSB PDB Mobile is still very much under development. Please let us know about any issues encountered in installation or use, especially in regard to formatting in the user interface.

RCSB PDB Mobile is also available the iPhone/iPod/iPad.

16-Jul-2013

Upcoming Meetings: ACA & ISMB/ECCB

ACA 2013

From July 20 - 24, the RCSB PDB will be at the 2013 Meeting of the American Crystallographic Association (ACA) in Honolulu, Hawaii.

Stop by exhibition booth 101 to pick up new materials and to meet with RCSB PDB Director Helen Berman, John Westbrook, and the PSI Structural Biology Knowledgebase (PSI SBKB)'s Margaret Gabanyi. View demonstrations of the new wwPDB Deposition and Annotation System, and Skype with RCSB PDB Annotators at Rutgers. The full list of activities below is also available as a PDF.

The RCSB PDB Poster Prize will also be awarded to recognize a student poster presentation involving macromolecular crystallography.


3DSig and ISMB/ECCB 2013

The International Society for Computational Biology and the European Conference on Computational Biology will meet July 19-23 in Berlin, Germany (ISMB/ECCB). RCSB PDB presentations will include What Bioinformaticians need to know about digital publishing beyond the PDF (Associate Director Phil Bourne) and New tools and visualization features at the RCSB PDB (Peter Rose). Get more conference details with the ISMB technology track schedule.

At the ISMB Special Interest Group meeting Bioinformatics Open Source Conference (BOSC), Andreas Prlić will present Ten simple rules for the open development of scientific software. Get more conference details with the BOSC schedule.

At the 3Dsig:Structural Bioinformatics & Computational Biophysics satellite meeting, Associate Director Stephen Burley will present a keynote presentation and poster on wwPDB: Ensuring a freely accessible, singular archive of high quality macromolecular structure information, and Peter Rose will present A survey of protein stoichiometry and symmetry in the PDB as a talk and a poster. The 3DSig poster Aligning subunits of internally symmetric proteins with CE-Symm by Spencer Bliven will also be presented. Associate Director Phil Bourne is one of the 3Dsig Program Chairs. Get more conference details with the 3Dsig schedule.

The RCSB PDB Poster Prize will be awarded for the best student poster presentation in the category of Protein Structure and Function Prediction and Analysis. 

09-Jul-2013

Spring Newsletter Published

Newsletter Cover

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Newsletter Cover.

The summer 2013 issue (HTML | PDF) has been published.

The newsletter highlights wwPDB news and milestones, past and future meeting activity, RCSB PDB Mobile for Android, and more.  

The Education Corner highlights the RCSB PDB's visit to the National Science Teachers Association meeting.

With RCSB PDB news and updates so readily available through electronic methods, we have decided to cease printing the paper edition of the quarterly newsletter. The current issue will be the last that is printed and mailed to our subscribers.

The newsletter will still be published online. We encourage all of our readers to sign up for quarterly newsletter electronic updates.

Past issues of the newsletter are available online

09-Jul-2013

Beta version #3 of RCSB PDB Mobile for Android

Beta version #3 of RCSB PDB <i>Mobile</i> for Android

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Beta version #3 of RCSB PDB Mobile for Android

The beta #3 Android version of RCSB PDB Mobile app is available for download. This update fixes some bugs and includes some minor UI changes.

RCSB PDB users with Android phones or tablets using version 2.3 or higher of the Android OS satisfying the testing requirements can download beta version #3 of RCSB PDB Mobile.

This edition of RCSB PDB Mobile is still under development. Please let us know about any issues encountered in installation or use, especially in regard to formatting in the user interface.

RCSB PDB Mobile is also available the iPhone/iPod/iPad. 

02-Jul-2013

Build 3D Paper Models at 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.

A new Paper Models page offers PDFs that can be used to build 3D models of DNA, tRNA, dengue virus, and the HIV capsid. A video demonstrates how to fold the DNA model.


The HIV capsid model (PDF) is based on the landmark structures recently released in the PDB archive and described in July's Molecule of the Month.

Other PDB-101 resources include:

  • In addition to  paper models, other Educational Resources include posters, animations, and classroom lessons and activities.
  • Author Profiles offer historical and educational timelines of the structures associated with a particular researcher. Example profiles and searches for authors and structural genomics centers are available.
  • Other Molecule of the Month articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.
  • Structural View of Biology. Built around the Molecule of the Month series, this feature promotes a top-down exploration of the PDB. Readers can travel through high-level functional categories (such as Protein Synthesis and Health and Disease) and descriptive subcategories (like Replication or Immune System) to access relevant articles that describe molecules in simple terms and provide specific examples.
  • Understanding PDB Data is 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 visit PDB-101 from the main RCSB PDB site, click on the blackboard PDB-101 logo or its related widget in the left-hand menu. This view offers easy navigation: select any Molecule of the Month article from the top bar pulldown menu or choose one of the tabs to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website. 



25-Jun-2013

Keep Up-to-Date with the RCSB PDB

Keep up to date with RCSB PDB News

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Keep up to date with RCSB PDB News.

The RCSB PDB serves a wide variety of users interested in biology, including researchers, teachers, students, and the general public. To help keep our different user communities informed about RCSB PDB activities, we rely on a number of web- and email-based communication methods, including social media.

18-Jun-2013

Create High Resolution Images

Image of a heme in hemoglobin structure 4hhb created with Ligand Explorer.

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Image of a heme in hemoglobin structure 4hhb created with Ligand Explorer.
Image from the Molecule of the Month article on Transfer-Messenger RNA.

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Image from the Molecule of the Month article on Transfer-Messenger RNA.

Create or download publication-quality pictures of biomacromolecules with the RCSB PDB.

Several interactive, Java-based tools1 can be used to visualize PDB data and create pictures.  Protein Workshop offers easily customized views; Simple Viewer utilizes a quick ribbon display; and Ligand Explorer visualizes the interactions of bound ligands in protein and nucleic acids structures.

Each program can be used to create and save high-resolution images in JPEG, PNG, and TIFF formats. Using the Save Image dialog box from the File menu, users can specify the width and height of an image in pixels, inches, or millimeters.

From the educational PDB-101 site, high resolution TIFFs of Molecule of the Month illustrations can be downloaded and used in presentations and publications. The high resolution files are linked from each article, and available as an archive.

PDB-101 posters, including The Structural Biology of HIV and Molecular Machinery: A Tour of the Protein Data Bank, can be saved as high or low resolution PDFs.

Citation and usage information can be found here

1J.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.  

11-Jun-2013

Search the PDB Using Drill-down Pie Charts

Use data distribution pie charts to find a set of PDB entries. This example shows how to find C5 symmetric homo-pentameric human proteins.

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Use data distribution pie charts to find a set of PDB entries. This example shows how to find C5 symmetric homo-pentameric human proteins.

Standard characteristics of PDB entries--organism, taxonomy, experimental method, X-ray resolution, release date, polymer type, EC, SCOP classification, protein symmetry, and protein stoichiometry--are used to create searchable data distribution summaries. 

The Explore Archive widget on the home page provides a quick statistical overview of the PDB. Browse the charts individually, or view them all together by clicking on the "Show all" link. Clicking on a pie chart image will display a more detailed graphic that lists the percentages for the categories shown.  Selecting one of the listed results will launch the corresponding structures in the Query Results Browser.

Data distribution drill-downs can also be used to refine search results and to explore the latest weekly update of PDB entries.

Any combination of categories is possible.  Users can drill-down to quickly access high resolution entries from a structure type search; human-related entries from a sequence search; or the most recent PDB entries containing a particular ligand.

For example, selecting the following drill-down options will quickly find C5 symmetric homo-pentameric human proteins:

Step 1: Protein Symmetry Cyclic
Step 2: Protein Symmetry C5
Step 3: Protein Stoichiometry Homomer
Step 4: Protein Stoichiometry A5
Step 5: Organism Homo sapiens

These charts can be hidden from the query results for users who want to only view the individual entries.

11-Jun-2013

New Paper: Trendspotting in the PDB

A new paper from the RCSB PDB has been published that analyzes PDB data to identify developments and trends in structural biology:

Trendspotting in the Protein Data Bank

Helen M. Berman, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo, Shuchismita Dutta, Sutapa Ghosh, Brian P. Hudson, Catherine L. Lawson, Ezra Peisach, Andreas Prlić, Peter W. Rose, Chenghua Shao, Huanwang Yang, Jasmine Young, Christine Zardecki

FEBS Letters 587: 1036-1045.
doi: 10.1016/j.febslet.2012.12.029

A full list of RCSB PDB publications is available.


04-Jun-2013

Map PDB Structures to Full-length Protein Sequences

Protein Feature View from 2xv3's Structure Summary page

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Protein Feature View from 2xv3's Structure Summary page.
Protein Feature View for all entries with UniProtKB ID Q13627. This image can be exported as an SVG file.

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Protein Feature View for all entries with UniProtKB ID Q13627. This image can be exported as an SVG file.

The Protein Feature View visually summarizes how a full-length protein sequence from UniProtKB corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are also displayed.

For individual entries, the Protein Feature View is available from the Molecular Description Widget on Structure Summary pages. The example shown for PDB ID 2vx3 illustrates how the ranges of a protein that have been observed in an experiment (in blue) correspond to the full length UniProtKB sequence (in grey). The secondary structure information from the PDB entry is also shown (helices in red, beta strands in yellow).

Various features that are known for the UniProtKB sequence are displayed in green as they correlate with regions in the PDB entry. Protein modifications and active site residues (from UniProtKB and the PDB entry) are also annotated. Moving the mouse cursor over the "lollipops" displays the residue label. Mousing over the images shown in the "Secstruc" row reveals secondary structure information from the entry.

This view can be expanded to map all PDB entries related to a single UniProtKB sequence by selecting the Protein Feature View link shown in this widget. By default, a few representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available. Selecting the plus sign or the "Show All" button will expand thew view to show all related PDB chains, which can then be sorted by resolution, length, and release date. These Protein View images can be exported as Scalable Vector Graphics (SVG) files.

The PDB to UniProtKB mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

28-May-2013

Browse the Anatomical Therapeutic Chemical Classification System to Find Structures

Use the Anatomical Therapeutic Chemical Classification Browser to find PDB structures

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Use the Anatomical Therapeutic Chemical Classification Browser to find PDB structures

RCSB PDB's Browse Database feature explores the PDB archive using different hierarchical trees. The WHO Collaborating Centre for Drug Statistics Methodology's Anatomical Therapeutic Chemical (ATC) classification system organizes drugs into five levels according to the organ or system on which they act and/or their therapeutic and chemical characteristics. The RCSB PDB database can be browsed using this system.

Select the ATC tab from the Browse Database interface to navigate through the drug classification hierarchy, view the number of associated PDB structures, and access the related entries.

The browser opens up the top level in the hierarchy. Clicking on the arrow/folder icons expands the respective nodes. Clicking on the name of the node will retrieve all PDB IDs associated with that ATC code.

Structures having a particular ATC code (e.g., A12CC05) or name (e.g., Atorvastatin) can be be found using the browser search box.

Other Browse options include GO Terms, Enzyme Classification, Transporter Classification, Source Organism, Genome Location, MeSH terms, SCOP, and CATH.

21-May-2013

Web Services for Accessing PDB Data

Web Services can help software developers build tools that efficiently interact with PDB data. Instead of storing coordinate files and related data locally, Web Services let software tools access the RCSB PDB remotely. Detailed documentation for accessing these Web Services is available.

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.

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.

14-May-2013

Personalize the RCSB PDB

Saved Query Manager Features.  A) After saving a search to MyPDB, name it by clicking on the words `User Query` providing a more descriptive label.  B) The manager can be used to change email notification settings, run queries, and delete saved searches.

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Saved Query Manager Features.  A) After saving a search to MyPDB, name it by clicking on the words `User Query` providing a more descriptive label.  B) The manager can be used to change email notification settings, run queries, and delete saved searches.

Set up a MyPDB account to create a personalized version of the RCSB PDB that is accessible from any computer.

Use the MyPDB widget in the left-hand menu to create an account and then log in to access stored setting and functionalities:

  • Saved Query Manager. Use MyPDB to store any type of 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. For example, users who frequently search for zinc finger motif using Advanced Search (Sequence Features>Sequence Motif=CX{2,4}CX{12}HX{3,5}H) can store the search in MyPDB, name it "zinc finger," and then run the query at any time.
  • 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.

07-May-2013

New PDB-101 Features

New PDB-101 Features

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New PDB-101 Features

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

New features have been added:

In Educational Resources > Posters/Exhibits

  • The flyer What is a Protein? (PDF) gives an introduction to protein structure and function for beginners.
  • The Structures of the Citric Acid Cycle (PDF) illustrates the PDB structures involved in this metabolic pathway.

In Educational Resources > Activities/Lessons

  • DNA resources have been translated into Spanish, including the Molecule of the Month article (PDF) and the DNA paper model template (PDF).

Other PDB-101 resources include:

  • Author Profiles are a unique historical and educational tool that display a timeline of the structures associated with a particular researcher. Example profiles and searches for authors and structural genomics centers are available.
  • Other Molecule of the Month articles describe the structure and function of a molecule, offer interactive views and discussion topics, and links to specialized pages to help explore specific example structures.
  • Structural View of Biology. Built around the Molecule of the Month series, this feature promotes a top-down exploration of the PDB. Readers can travel through high-level functional categories (such as Protein Synthesis and Health and Disease) and descriptive subcategories (like Replication or Immune System) to access relevant articles that describe molecules in simple terms and provide specific examples.
  • Understanding PDB Data is 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 visit PDB-101 from the main RCSB PDB site, click on the blackboard PDB-101 logo or its related widget in the left-hand menu. This view offers easy navigation: select any Molecule of the Month article from the top bar pulldown menu or choose one of the tabs to jump to other sections. Select the blue RCSB PDB logo from the top of the page at any time to return to the main website.

30-Apr-2013

Updated Version of MAXIT Available

MAXIT Version 8 includes a new option to assign ligands the same chain IDs as the adjacent polymers and incorporates several fixes to bugs.

This command-line program can also be used to:

  • Read and write PDB and mmCIF format files, and translate between file formats
  • Perform consistency checks on coordinates, sequence, and crystal data
  • Automatically construct, transform, and merge information between formats
  • Align residue numbering in the coordinates with the sequence
  • Reorder and rename atoms in standard and nonstandard residues and ligands according to the Chemical Component Dictionary

Visit sw-tools.rcsb.org to download MAXIT and other programs for processing and curating PDB data.

23-Apr-2013

Rutgers Day (April 27)

Rutgers Day: April 27.
Rutgers Day: April 27.

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 Center for Integrative Proteomics Research'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. Admission and parking are both free.

23-Apr-2013

DNA Day 2013: April 25

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.

Celebrate by:

23-Apr-2013

Beta Test RCSB PDB Mobile for Android

The beta #1 Android  version of RCSB PDB Mobile app available for download.

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The beta #1 Android version of RCSB PDB Mobile app is available for download.

RCSB PDB users with Android phones or tablets using version 2.3 or higher of the Android OS can download beta version #1 of RCSB PDB Mobile.

This free app provides fast, on-the-go access to the RCSB PDB. Options are available to search the entire PDB database, view the latest protein and nucleic acid structures released, access MyPDB, view the entire catalog of Molecule of the Month articles, and more. Structures can be interactively explored using the molecular viewer NDKMol (courtesy of Dr. Takanori Nakane, Kyoto University).

The Android edition of RCSB PDB Mobile is still under development. Please let us know about any issues encountered in installation or use, especially in regard to formatting. This beta release will "time out" in 2 months, by which time we anticipate the next generation app will be available from the Google Play Store.

16-Apr-2013

Upcoming Meeting: Experimental Biology and ASBMB

Experimental Biology conference.

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Experimental Biology conference.
ASBMB Meeting.

ASBMB Meeting.

The RCSB PDB will be exhibiting along with the PSI SBKB at the American Society for Biochemistry and Molecular Biology's Annual Meeting (ASBMB, April 20-24, Boston, MA), which is being held in conjunction with the Experimental Biology conference. Stop by booth #573 to meet with RCSB PDB staff, explore new website features, and pick up the new Structures of the Citric Acid Cycle flyer (PDF).

Also at this meeting, RCSB PDB Director Helen M. Berman will receive the 2013 DeLano Award for Computational Biosciences. She will present PDB as a public resource for enabling protein science on Monday April 22 (Room 258, Level Two - East Boston Convention and Exhibition Center).

The Award, established by family, friends and colleagues to honor the legacy of Warren L. DeLano, recognizes scientists for the most accessible and innovative development or application of computer technology to enhance research in the life sciences at the molecular level.

This 2013 award honors Prof. Berman's efforts to make data universally available. For more information, please see ASBMB Today.

09-Apr-2013

Visit the RCSB PDB at NSTA

Visit the RCSB PDB at NSTA.

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Visit the RCSB PDB at NSTA.
NSTA Meeting.

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NSTA Meeting.

From April 11-13, the RCSB PDB will be at the 2013 meeting of the National Science Teachers Association in San Antonio, TX.

Stop by exhibition booth 1544 to meet for demonstrations and PDB-101 materials, including the new flyers What is a Protein? (PDF) and The Structures of the Citric Acid Cycle (PDF).

On Saturday, April 13, we'll host a workshop on Exploring Proteins and Nucleic Acids at the PDB in Convention Center Room 214C at 12pm.

We'll be posting news on Facebook and Twitter throughout the meeting.

09-Apr-2013

Spring Newsletter Published

Spring 2013 Newsletter.

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Spring 2013 Newsletter.

The spring 2013 issue (HTML | PDF) has been published.

The newsletter describes new website features, the Biologically Interesting molecule Reference Dictionary, and more. The Education Corner highlights the RCSB PDB help desk.

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

02-Apr-2013

Search, View Annotations, and Visualize Peptide-like Antibiotic and Inhibitor Molecules

Autosuggestions from a Simple Search for actinomycin
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Autosuggestions from a Simple Search for actinomycin
Advanced Search options for querying BIRD
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Advanced Search options for querying BIRD
BIRD widget from PDB ID 1a7y.
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BIRD widget from PDB ID 1a7y

BIRD refers to the wwPDB's Biologically Interesting Molecule Reference Dictionary, and contains information about the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive.

An example of a BIRD molecule is April's Molecule of the Month: actinomycin.

New RCSB PDB website features utilize BIRD data to provide improved searching and visualization options for these molecules:

Search BIRD Molecules

Simple Search
Biologically interesting Molecules from BIRD can be searched by typing a name (vancomycin), a BIRD ID (PRD_000204), type (glycopeptide), or class (antibiotic) in the top search bar. Suggestions will appear under the BIRD Molecules category.

Advanced Search
Biologically interesting Molecules from BIRD can also be searched from the advanced search menu.  Search by text/name, BIRD type (structural classification of the molecule), or BIRD class (broad definition of the molecule function).

View Annotations from BIRD

The BIRD widget on an entry's Structure Summary page will display the ID, image, name, type, class, and chain location for any such molecules in the entry.   Ligand Explorer can be launched to view the molecule and binding site in 3D.

As with other Structure Summary page features, the examples displayed (ID, name, type, and class) can be used to find other PDB entries with the same characteristics.

Protein Workshop view of actinomycin D as seen in PDB ID 1a7y.
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Protein Workshop view of actinomycin D as seen in PDB ID 1a7y.
Ligand Explorer view of Vancomycin PRD_000204.
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Ligand Explorer view of Vancomycin PRD_000204.

Protein Workshop view of vancomycin PRD_000204 as seen in PDB ID 1pnv.
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Protein Workshop view of vancomycin PRD_000204 as seen in PDB ID 1pnv.

Visualize BIRD Molecules

Ligand Explorer

Ligand Explorer can be launched from the BIRD Widget to visualize these molecules and their binding sites. The program can center on other molecules by clicking on a name or identifier from the left hand menu. Intermolecular interactions such as hydrogen bond or hydrophobic interactions and a binding site surface can be turned on for the active ligand.

Protein Workshop

In Protein Workshop, BIRD molecules are listed in the right hand menu and can be manipulated as with any other macromolecule chain or ligand. Protein Workshop can be launched from any entry's Structure Summary page.


26-Mar-2013

3D Visualization of Protein Symmetry

To create this image, select the 'View in 3D' link for PDB ID 1G63, and then select Jmol options polyhedron: on; axes: on; style: CPK; color: symmetry; and deselect background: black.

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To create this image, select the 'View in 3D' link for PDB ID 1G63, and then select Jmol options polyhedron: on; axes: on; style: CPK; color: symmetry; and deselect background: black.

To facilitate the exploration of symmetry, several options are available from the 3D Jmol views of structure:

  • Default Orientations: Users can toggle between canonical views of structure that highlight symmetry: sides and back, and along unique n-fold symmetry axes.
  • Symmetry axes and polyhedra. Symmetry axes and symbols representing folds (dyad for 2-fold, triad for 3-fold axis, or in general a polygon for n-fold axis) can be displayed with a structure.  Users can select to view the protein enclosed in a polyhedron that matches its symmetry.
  • Colored by symmetry or subunit.  Structures can be colored by symmetry (see the list of color schemes used), sequence (subunits with >= 95% sequence identity shown in the same color), or by subunit.
  • Pseudosymmetry. The default view shows symmetry based on a 95% sequence identity threshold. Since some structures will display pseudosymmetry when using a 30% sequence identity threshold, an option lets users toggle between the two options.

To access Jmol on the RCSB PDB site, select the "View in 3D" link on any entry's Structure Summary page. Protein symmetry is calculated for all entries containing at least one protein chain, including asymmetric units and all biological assemblies (except for entries split among several PDB files due to their size).

19-Mar-2013

Visit the San Diego Festival of Science and Engineering on March 23

Visit the San Diego Festival of Science and Engineering on March 23.
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Visit the San Diego Festival of Science and Engineering on March 23

On Saturday March 23, visitors to the RCSB PDB booth at the San Diego Festival of Science and Engineering's EXPO DAY will learn about the basic building blocks of life by building a 3D model of DNA and a small zinc finger protein. They can also watch animations of 3D proteins and nucleic acids, and take home posters and other materials about these fascinating structures.

EXPO DAY is the grand-slam-science-finale to a week of big events at San Diego State University, Balboa Park and California State University San Marcos.

Over 27,000 kids, families, scientists, engineers, educators, and other community members are expected to take part in this year's EXPO DAY, a free-to-the-community event! 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 PDB-101.

19-Mar-2013

Distribution of PDB Data by Protein Stoichiometry and Symmetry

Drilling down through PDB data distributions.

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Drilling down through PDB data distributions.

Distribution drill-downs for protein stoichiometry and symmetry (at 95% sequence identity threshold) have been added to the Explore Archive widget on the home page. The stoichiometry and symmetry information comes from the first biological assembly associated with the entry.

The drill-downs can be applied successively. For example to find C5 symmetric homo-pentameric human proteins one would use the following sequence of drill-downs:

Step 1: Protein Symmetry Cyclic
Step 2: Protein Symmetry C5
Step 3: Protein Stoichiometry Homomer
Step 4: Protein Stoichiometry A5
Step 5: Organism Homo sapiens

Drill-downs, including options for stoichiometry or symmetry, can also be used to further refine search results from the query result browser page.

Advanced Search can also be used to search for structures based on protein stoichiometry and symmetry.

12-Mar-2013

Access Drugs and Drug Targets in the PDB

The example shows the auto-complete suggestions for stereoisomers when searching Ibuprofen.

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The example shows the auto-complete suggestions for stereoisomers when searching Ibuprofen.
DrugBank widget for ibuprofen.

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DrugBank widget for ibuprofen.

New features for exploring drugs found in PDB entries were recently added to the website.

Stereoisomers. The integration of drug and drug target data from DrugBank (www.drugbank.ca) has been extended to include stereoisomer matches. Searches for a given drug name will now return the different stereoisomers of the drug. For example, a Simple Search for Ibuprofen in the top bar will suggest the different stereoisomers associated with the drug.

DrugBank Widget. A new Drug Info widget available from Ligand Summary pages lists the corresponding data from DrugBank (when available). The widget contains DrugBank ID, drug name, groups, brand name, and more, with links to the corresponding data at DrugBank. A sequence search based on the drug target sequence can be launched from this widget.  For an example, see the Ligand Summary page for IBP (ibuprofen).

Browse Database using ATC. The WHO Collaborating Centre for Drug Statistics Methodology's Anatomical Therapeutic Chemical (ATC) classification system organizes drugs into five levels according to the organ or system on which they act and/or their therapeutic and chemical characteristics. The RCSB PDB database can now be browsed using this system. Select the ATC tab from the Browse Database interface to navigate through the drug classification hierarchy, view the number of associated PDB structures, and access the related entries.

05-Mar-2013

New Website Release

New Ligand Explorer view of biotin (PDB ID 1STP), displayed with the default options of a solid surface, colored by hydrophobicity, with a distance threshold of 6.5 Å

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New Ligand Explorer view of biotin (PDB ID 1STP), displayed with the default options of a solid surface, colored by hydrophobicity, with a distance threshold of 6.5 Å
PDB-101 has new tabs for easier access to Educational Materials, Molecule of the Month, Understanding PDB Data, and Author Profiles. A

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PDB-101 has new tabs for easier access to Educational Materials, Molecule of the Month, Understanding PDB Data, and Author Profiles. A "PDB-101 News" section has been added.

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

  • The Simple Search available from the top menu bar has a cleaner and simpler look and feel. The search form offers the same search suggestion capabilities.
  • A new Browse Database option can be used to find structures using the Anatomical Therapeutic Chemical (ATC) Classification System for drugs from the WHO Collaborating Centre for Drug Statistics Methodology.
  • Jmol pages now include an updated Display Options menu, new scripting options, tabs for domains and ligands, and the JavaScript beta version of Jmol.
  • Information about protein stoichiometry and symmetry have been integrated into drill down charts and Advanced Search.  Symmetry features can be highlighted in Jmol.

 

See the What's New page for more new features and examples.

26-Feb-2013

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

Browsing through molecular functions

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Browsing through molecular functions.

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

Click Browse from the top of every RCSB PDB page to access this feature, and then the desired Browser Tab to start searching.

19-Feb-2013

Build complex queries with Advanced Search

Click on the magnifying glass icon from the top menu bar to access Advanced Search.
Click on the magnifying glass icon from the top menu bar to access 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  . New options include quick searches by experimental and/or molecule type, searches based on structure determination method, and the ability to find structures containing interresidue connectivity (LINK records) that cannot be inferred from the primary structure.

Currently, users can build searches based on:

  • Quick Search: retrieve all PDB entries or a subset based on experimental method or molecule type
  • ID(s) and Keywords: PDB, PubMed, UniProtKB, Pfam IDs; text and keyword searching
  • Structure Annotation: structure title, description; and macromolecule name
  • Deposition: author name; deposit, release, and revision date; latest released and modified structures; Structural Genomics Project
  • Structure Features: macromolecule type; number of chains (asymmetric unit or biological assembly), entities, models, and disulfide bonds; interresidue connectivity (LINK records); molecular weight; secondary structure content; secondary structure length; SCOP, CATH, taxonomy
  • Sequence Features: sequence; translated nucleotide sequence; sequence motif; chain length; genome location
  • Chemical Components: name; ID; InChi descriptor; SMILES/SMARTS; molecular weight; chemical formula; chemical component type; binding affinity; has ligands; has modified residues; sub-components
  • Biology: Source; expression organism; Enzyme Classification; biological process; cell component; molecular function; Transporter Classification
  • Methods: experimental method; X-ray resolution, R factor, diffraction source, structure determination method, 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.

12-Feb-2013

Poster Prize Awarded at AsCA

Congratulations to Yohta Fukuda for Atomic resolution structure of copper-containing nitrite reductase provides insights into common properties of type 2 copper-containing enzymes.

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Congratulations to Yohta Fukuda for Atomic resolution structure of copper-containing nitrite reductase provides insights into common properties of type 2 copper-containing enzymes.
AsCA.

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AsCA.

The RCSB PDB Poster Prize went to Yohta Fukuda at the Joint Meeting of the Asian Crystallographic Association (AsCA), Society of Crystallographers in Australia and New Zealand (SCANZ) and the BRAGG Symposium (December 2 - 6, 2012, Adelaide, Australia) for:

Atomic resolution structure of copper-containing nitrite reductase provides insights into common properties of type 2 copper-containing enzymes
Yohta Fukuda,1 Taro Tamada,2 Hideto Takami,3 Tsuyoshi Inoue,1 Masaki Nojiri1

1Osaka University
2Japan Atomic Energy Agency
3Japan Agency of Marine-Earth Science and Technology

Yohta will receive  Computational Structural Biology (Torsten Schwede, Manuel C. Peitsch, editors) and International Tables of Crystallography Volume F.

Many thanks to Charlie Bond (University of Western Australia) and AsCA.

All 2012 awardees are listed on the RCSB PDB website.

05-Feb-2013

Author Profiles: Timeline Display of a Researcher's Structures

Author Profiles provide a timeline display of a researcher's structures.

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Author Profiles provide a timeline display of a researcher's structures.
To access this feature, select the link from the left hand RCSB PDB menu, or from the PDB-101 Features pull-down menu.

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To access this feature, select the link from the left hand RCSB PDB menu, or from the PDB-101 Features pull-down menu.

Author Profiles are a unique historical and educational tool offering a timeline display of all structures associated with a particular researcher. Structures are sorted by deposition date, with the first instance of a protein or protein complex highlighted. Images are linked to the Structure Summary page for the entry.

A search box is provided to search by author or structural genomics center name. Author Profile URLs are permanent links that can be copied and shared.

For an example, visit A.M. Gronenborn's Author Profile.

05-Feb-2013

News Reader Survey

Please take our brief survey about RCSB PDB news and the Newsletter.

Please take our brief survey about RCSB PDB news and the Newsletter. Your responses are greatly appreciated!

29-Jan-2013

Visit the Biomolecular Discovery Dome at Biophysical Society

See proteins and molecular machines like you never have before in the Biomolecular Discovery Dome.

See proteins and molecular machines like you never have before in the Biomolecular Discovery Dome.

See proteins and molecular machines like you never have before in the Biomolecular Discovery Dome, an audio-visual immersion experience that takes you inside the world of cells and viruses.

The Biomolecular Discovery Dome will be located in the Exhibit Hall at the Biophysical Society Meeting Sunday, February 3 - Tuesday, February 5 (10:00 AM - 5:00 PM) and Wednesday, February 6 (9:00 AM - 1:00 PM) in Philadelphia, PA.

Short films scheduled to appear include:

  • Viruses for Good and Evil
  • NANOPLANET: An Expedition to the Cell
  • The Rod Sensory Cilium and Its Disruption in Retinal Neurodegeneration
  • How HIV Replicates
  • Trypanosomes: Their Flagella, and How They Move

The Biomolecular Discovery Dome is sponsored by the Biophysical Society's Public Affairs Committee.

29-Jan-2013

Join the RCSB PDB Team

The RCSB PDB is looking for a Lead Web Architect.

Join the RCSB PDB Team.

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Join the RCSB PDB Team.

22-Jan-2013

Portable Molecules (of the Month)

Read Molecule of the Month articles in RCSB PDB Mobile.

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Read Molecule of the Month articles in RCSB PDB Mobile.

The RCSB PDB Mobile app for Apple iOS provides fast access to PDB searching and molecular visualization.

Click on the App Store link to access the free download of RCSB PDB Mobile.
Click on the App Store link to access the free download of RCSB PDB Mobile.

The entire catalog of Molecule of the Month articles is available. Each feature describes important biological molecules and how they function with descriptive text and illustrations. The molecules used as examples in the articles can be further explored and viewed in 3D.

Further information is available from the RCSB PDB Mobile information page, PDF flyer, and FAQ.

A version of the app for the Android platform is in development.

22-Jan-2013

Revision History Widget

The Revision History widget box notes the changes made to an entry's mmCIF/PDBx file after the initial release.  Mousing over the text will display the details of the update.

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The Revision History widget box notes the changes made to an entry's mmCIF/PDBx file after the initial release.  Mousing over the text will display the details of the update.

Structure Summary pages offer a variety of information about an entry, organized into different widget boxes that can be moved around on the page. 

The Revision History widget box displays the details of changes made to an entry's mmCIF/PDBx file after the initial release. The details of these changes have been recorded in the category PDBX_VERSION since July 2011 (see the wwPDB website for more information).

These descriptions are more detailed than the information stored in REVDAT records, which indicate what records have been changed in the PDB format file for the entry.

The Revision History box shows the modification date and a summary description; mousing over the text provides additional details.

15-Jan-2013

Quick Tour of Search Results

View this video to see the different options available for exploring search results.

08-Jan-2013

Winter Newsletter Published

Winter 2013 newsletter cover.

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Winter 2013 Newsletter.

The winter 2013 issue (HTML | PDF) has been published.

The newsletter explores the 2012 Annual Report, 2012 deposition and access statistics, how to visually map PDB structures to sequences, and more.

wwPDB announcements are also included.

Features related to Data Query, Reporting, and Access highlight RCSB PDB Mobile, smart searching, PDB Data Overviews, and more.

The Education Corner, by Takanori Nakane (Kyoto University), describes his journey from medical school to molecular visualization development. Nakane's program NDKmol is part of the RCSB PDB Mobile app.

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

08-Jan-2013

News Reader Survey

News reader survey.

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News reader survey.

Please take our brief survey about RCSB PDB news and the Newsletter.  Your responses are greatly appreciated!

01-Jan-2013

Annual Report Published

This edition's Annual Report cover maps the proteins and chemical reactions involved with the citric acid cycle.  The proteins of the citric acid cycle were highlighted in the October 2012 Molecule of the Month.

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This edition's Annual Report cover maps the proteins and chemical reactions involved with the citric acid cycle.  The proteins of the citric acid cycle were highlighted in the October 2012 Molecule of the Month.

Download the 2012 Annual Report (PDF) for an overview of data deposition, query, outreach, and education activities.

The recently published Annual Report highlights the RCSB PDB's accomplishments for 2012. It also reviews topics ranging from deposition statistics to domain-based structural alignments to popular questions to popular help desk questions and answers.

wwPDB efforts, including the development of the Common Deposition and Annotation Tool, are also highlighted.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive. This edition, the RCSB PDB's thirteenth, is available as a PDF download from www.rcsb.org/ar12. If you would like a printed copy, please send your postal address to info@rcsb.org.