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Year 2014 News

Contents:

21-Oct-2014 Comparison Tool for Exploring Sequence and Structure Alignments
14-Oct-2014 Upcoming Meeting: SACNAS
07-Oct-2014 Fall Newsletter Published
30-Sep-2014 Map Structures to Sequences with Protein Feature View
23-Sep-2014 Paper Published: RCSB PDB Mobile
16-Sep-2014 Exploring Structure Quality
09-Sep-2014 Head Back to School with PDB-101
02-Sep-2014 Join the RCSB PDB Team
02-Sep-2014 Take the PDB-101 Survey
26-Aug-2014 Poster Prize Awarded at ISMB
26-Aug-2014 Announcement: Meeting on Hybrid Methods
19-Aug-2014 Poster Prize Awarded at IUCr
12-Aug-2014 New Website Release
05-Aug-2014 wwPDB Events at IUCr (August 5-12)
29-Jul-2014 Personalize the RCSB PDB
22-Jul-2014 Explore PDB Structures by Browsing Annotations
15-Jul-2014 RCSB PDB Leadership Transition
08-Jul-2014 Summer Newsletter Published
01-Jul-2014 Quick Tour of Search Results
24-Jun-2014 Depositing Data? Use the wwPDB Deposition & Annotation System
17-Jun-2014 HIV Video Challenge Awards
10-Jun-2014 Poster Prize Awarded at ACA
10-Jun-2014 Papers Published
03-Jun-2014 Vote Now!
27-May-2014 RCSB PDB Mobile for iOS and Android
20-May-2014 Special Events in Albuquerque at ACA 2014
20-May-2014 Art of Science Travels to Paris, France
13-May-2014 PDB Reaches 100,000
13-May-2014 Molecular Machinery Update
06-May-2014 Video Challenge for High School Students
29-Apr-2014 New Website Release
22-Apr-2014 Visit the USA Science and Engineering Festival Expo on April 26 & 27
22-Apr-2014 DNA Day 2014: April 25
15-Apr-2014 Resources for High School Video Challenge
08-Apr-2014 Spring Newsletter Published
01-Apr-2014 Build a Model of GFP
01-Apr-2014 Our Best Wishes to Phil
25-Mar-2014 Learn How to Create Molecular Animations
25-Mar-2014 The Art of Systems Biology and Nanoscience
18-Mar-2014 Visit the San Diego Festival of Science and Engineering on March 22
11-Mar-2014 Author Profiles: Timeline Display of a Researcher's Structures
11-Mar-2014 Meet the RCSB PDB Team
04-Mar-2014 Membrane Query and Annotation
25-Feb-2014 Video Challenge for High School Students
18-Feb-2014 Releasing Structures on Hold for Publication
11-Feb-2014 Find PDB Structures with Protein Purification Tags
04-Feb-2014 Tour of Ligand Deposition
28-Jan-2014 Binding Site Visualization
21-Jan-2014 Big Picture on Proteins
14-Jan-2014 Teacher Workshop in Boulder, Colorado
14-Jan-2014 RapiData 2014
07-Jan-2014 Winter Newsletter Published

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


21-Oct-2014

Comparison Tool for Exploring Sequence and Structure Alignments

ALT_TAG_HERE

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

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.

14-Oct-2014

Upcoming Meeting: SACNAS

SACNAS 2014 The RCSB PDB is hosting a session at the National Conference of the Society for Advancement of Hispanics/Chicanos and Native Americans in Science (SACNAS) that will take place October 16-18 in Los Angeles, CA.
Structural View of Biology: Explorations of Molecular Structure and Function
Thursday, October 16, 2014: 10:15 AM-11:45 AM
Los Angeles Convention Center 304A

This session will describe three aspects of research in structural and computational biology: how atomic structures of proteins are solved, how the Protein Data Bank has revolutionized the way researchers and students explore these structures, and how these structures are used to engineer new functions in proteins.

  • Introductory Remarks, Stephen K. Burley, PhD (Chair; RCSB PDB and Rutgers)
  • Amyloid Crystallography: Zapping Miniscule Crystals with Powerful X-Rays to Understand Molecular Mishaps in Disease, Rebecca Nelson, PhD (University of California, Los Angeles)
  • Protein Data Bank: Enabling Open Access to Macromolecular Structures, Helen M. Berman, PhD (RCSB PDB and Rutgers)
  • Towards overcoming the deficiencies of recently evolved biodegradation enzymes, Nancy Hernandez, BA (Rutgers)

07-Oct-2014

Fall Newsletter Published

2014q4 RCSB PDB NewsletterThe Fall 2014 issue of the RCSB PDB Newsletter is now available

Articles include Map Structures to Sequences with Protein Feature View; Inclusion of Large Structures in the PDB; Head Back to School with PDB-101; and more.

This issue's Education Corner highlights Molecular Visualization for the Masses: PDB Goes to Disneyland by Bob Hanson, St. Olaf College.

RCSB PDB's Newsletter is published online. Sign up to receive electronic updates each quarter.

Past issues of the newsletter are available.

30-Sep-2014

Map Structures to Sequences with Protein Feature View

RCSB PDB's Protein Feature View visually summarizes how a full-length protein sequence from UniProt 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.

The Protein Feature View was recently redesigned to improve readability and to add descriptions of protein function, subunit structure, domains information, and genomic exon structure.

Protein Feature View can be launched from the "Molecular Description" section of a Structure Summary page (see 2D5Z) as well as by searching for a UniProt ID (P69905) or Gene Symbol (HBA1). These Protein View images can be exported as Scalable Vector Graphics (SVG) files.

The PDB to UniProt mapping is based on the data provided by the SIFTS project.

Protein Feature View

Protein Feature View for UniProt ID P69905 showing the new Exon Structure track

23-Sep-2014

Paper Published: RCSB PDB Mobile

A new Bioinformatics paper describes how the iOS/Android app enables fast and convenient access to RCSB PDB data and services:  

RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
(2014) Bioinformatics doi:10.1093/bioinformatics/btu596.

This universal app enables the general public, researchers and scholars to search the PDB and visualize protein structures over a WiFi or cellular data connection.

Freely available for the iPhone/iPod/iPad and Android (2.3.3 and above), RCSB PDB Mobile can be used to search the entire PDB database, view the latest released structures, access  MyPDB accounts, and view the entire catalog of Molecule of the Month articles.

Interactive 3D visualization utilizes the program NDKMol (courtesy of Dr. Takanori Nakane, Kyoto University). Interactively view a molecule from by entering a PDB ID or launching the viewer from the search results. These views can be saved as images.

RCSB PDB Mobile can be downloaded from the Apple Store and Google play. All RCSB PDB publications are listed online.

16-Sep-2014

Exploring Structure Quality

Structure Summary pages for X-ray crystal structures provide access to validation information based upon the recommendations of the wwPDB X-ray Validation Task Force:

  • The "slider" graphic displayed on the page gives an indication of the quality of the determined structure as compared with previously deposited PDB entries using several important global quality indicators
  • The full PDB Validation Report PDF, which contains the slider graphic and other information to provide an assessment of the quality of a structure and highlight specific concerns (visit the wwPDB for more information)
  • A new PDF report containing Ramachandran plots created using MolProbity (version 4.02b). Ramachandran plots provide an independent method to evaluate the conformational quality of protein structures, and offer a visual representation of any outliers tabulated in the Validation Report PDF.  For more information about MolProbity, see Chen et al. (2010) Acta Cryst D66:12-21.

Previously, Ramachandran plots were located on the Structure Summary Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.



Ramachandran plots for entry for 1CBS

Ramachandran plots for entry 1cbs as created by MolProbity.

09-Sep-2014

Head Back to School with PDB-101

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.

New features include the new Molecular Machinery poster and the GFP paper model.

Other PDB-101 resources include:

  • Educational Resources include posters, animations, paper models, 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.
  • 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.
  • The Structural View of Biology Browser 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.
  • Video Challenge. RCSB PDB challenged high school students to tell a molecular story about HIV/AIDS, with great results.
  • EduForum. Start a discussion about structural biology.

To visit PDB-101 from the main RCSB PDB site, click on the blackboard PDB-101 logo. 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.


Full Molecular Machinery

Download this poster from PDB-101 or enter a drawing for a printed copy by taking our quick survey.

02-Sep-2014

Join the RCSB PDB Team

The RCSB PDB is looking for a Senior Java Web Developer. Applications should be submitted online

Code with Us

Join the RCSB PDB as a Senior Java Web Developer.

02-Sep-2014

Take the PDB-101 Survey

Please answer a few questions about PDB-101 usage. Enter your email address to win a 2014 Molecular Machinery poster.

Your responses are greatly appreciated!

26-Aug-2014

Poster Prize Awarded at ISMB

At the Intelligent Systems for Molecular Biology conference (ISMB; July 12-15; Boston, MA), the RCSB PDB Poster Prize was awarded to Thomas Hoffmann for:

Structural Analysis and Remodeling of T-Cell Receptors
Thomas Hoffmann and Iris Antes, Technische Universität München, Germany

Many thanks to the the International Society for Computational Biology and the ISMB poster judges.

All 2014 awardees are listed on the RCSB PDB website and will receive an educational book. RCSB PDB Poster Prize was awarded to Thomas Hoffmann

26-Aug-2014

Announcement: Meeting on Hybrid Methods

Meeting on Hybrid Methods 2015

Hybrid Methods in Structural Biology is organized by Jens Meiler, Patrick Cramer and Ron A. Milligan.

DEADLINES:

  • Scholarship Deadline: Nov 6, 2014
  • Discounted Abstract Deadline: Nov 6, 2014
  • Abstract Deadline: Dec 9, 2014
  • Discounted Registration Deadline: Jan 8, 2015

As we study the structure and dynamics of more and more complex systems to better understand their biological function, each individual technology in the structural biology toolbox approaches its limitations. These limitations include size of the system, timeline of motions, spatial and/or temporal resolution, and ensemble averaging. Further, each individual method perturbs the system in a different way to enable or facilitate its analysis. This includes for example the introduction of spin labels to perform EPR experiments, the reconstitution of membrane proteins in micelles for NMR spectroscopy, the introduction of entire domains to stabilize proteins in certain conformations for crystallization, or a simplified force field in computation. As systems become more challenging, the perturbations tend to get more drastic, complicating the interpretation of results. Only at the intersection of several techniques it becomes possible to distinguish information that is biologically relevant from perturbations introduced by any individual approach. Moving forward, hybrid methods and integrated methods in structural biology play a key role in studying complex systems verifying each other's results. The objective of this meeting is two-fold: 1) To discuss novel and potentially disruptive technologies and/or combinations thereof to be added to the hybrid methods toolbox; and 2) To illustrate and discuss application of hybrid methods to important biological systems. These objectives will be achieved not only by a line-up of exceptional oral presentations, but also by a prominently placed poster session, discussions in panel format, and tutorial sessions introducing new software algorithms.

For more information, visit www.keystonesymposia.org/15C2.

19-Aug-2014

Poster Prize Awarded at IUCr

At the General Assembly and Congress of the International Union of Crystallography (IUCr; August 5-12; Montreal, Quebec, Canada), the RCSB PDB Poster Prize was awarded to Josephine H. Leung for:

Transhydrogenase coupling proton translocation and hydride transfer
Josephine H. Leung,1 Lici A. Schurig-Briccio,2 Mutsuo Yamaguchi,1 Arne Moeller,3,4 Jeffrey A. Speir,3 Robert B. Gennis,2 Charles D. Stout1
1Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
2Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
3National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA
4Current address: DANDRITE Group Leader, Aarhus University, Gustav Wiedsvey 14, 8000 Aarhus C, Denmark

Many thanks to the poster prize chair Alba Guarne (McMaster University) and judges Gerard Audette (York University), Fasseli Coulibaly (Monash University), Jean-François Couture (University of Ottawa), Francois Ferron (Laboratoire CNRS), Zongchao Jia (Queen's University), Clara Kielkopf (University of Rochester), Bostjan Kobe (University of Queensland), Pedro Pereira, Sandra Ribeiro-Macedo (Instituto De Biologia Molecular E Celular), Martin Schmeing (McGill University), Peter Stogios (University of Toronto), Nuria Verdaguer (Institut de Biologia Molecular de Barcelona), Alice Vrielink (University of Western Australia), Joe Wedekind (University of Rochester).

All 2014 awardees will be listed on the RCSB PDB website and will receive an educational book.

The RCSB PDB also participated in several other events at the IUCr meeting; pictures are online at the wwPDB and RCSB PDB Facebook pages.

RCSB PDB Poster Prize was awarded to Josephine H. Leung

12-Aug-2014

New Website Release

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

  • A new Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.
  • Protein Feature View has been redesigned to improve readability and to add descriptions of protein function, subunit structure, and domains from UniProt, and an Exon Structure track from the gene mapping described above.
  • Ramachandran plots created by MolProbity are available from Structure Summary pages for X-ray crystal structures
  • The average temperature (B) factor has been added to the Refinement Details section of the tabular report creation options.
  • The website has been redesigned so that a new navigation menu at the top of the website replaces the traditional left-hand menu.

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

05-Aug-2014

wwPDB Events at IUCr (August 5-12)

Meet wwPDB members from around the globe at the 23rd General Assembly and Congress of the International Union of Crystallography (IUCr, August 5-12, 2014) in Montreal, Quebec, Canada.

Come to exhibition stand 114 to receive a special sticker celebrating your contributions to the 100,000+ structures in the PDB archive.

Other wwPDB events include:

Thursday August 7

  • Poster: The New wwPDB Deposition and Annotation System presented by John Westbrook (RCSB PDB) BM.P54.A536


Saturday August 9

  • Oral Presentation: The history of the PDB as a public resource for enabling science by Helen M. Berman (RCSB PDB) in MS61 The Beginnings Of Biological Crystallography (1:45 - 4:20pm) in Room 517d.
  • Poster: Educational Outreach and User Training at the Worldwide Protein Data Bank (MS84.P01.B415) presented by Matthew Conroy (PDBe) and Christine Zardecki (RCSB PDB).
  • Poster: Japanese Science & Technology with Crystallography (MS86.P17.B445) presented by Atsushi Nakagawa (PDBj).


Monday August 10

  • Oral Presentation: Educational Outreach and User Training at the Worldwide Protein Data Bank (MS84.P01.B415) by Matthew Conroy (PDBe) and Christine Zardecki (RCSB PDB) in MS84 Crystallography Education and Training in the 21st Century: New Pedagogies, New Paradigms, Part I (9:40am - 12:15pm) in room 517a.


Tuesday August 12

  • Oral Presentation: New wwPDB validation pipelines for X-ray, NMR and 3DEM structures by Sameer Velankar (PDBe) in MS100 Beginner's Guide to Validation of Crystallographic Results on (9:40am - 12:15pm) in room 517a.


Depositor Sticker

Visit exhibition stand 114 for a sticker highlighting how many structures you've deposited.

29-Jul-2014

Personalize the RCSB PDB

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.

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.

22-Jul-2014

Explore PDB Structures by Browsing Annotations

RCSB PDB's Browse Database feature offers access to structures in the PDB archive using different hierarchical trees.

Browsers are available to find structures organized around the following classifications:

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

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.

15-Jul-2014

RCSB PDB Leadership Transition

It is announced today that Dr. Stephen K. Burley will become the Director of the RCSB Protein Data Bank organization, effective July 2014. Burley is an internationally recognized physician-scientist, and an authority on structural biology, drug discovery, clinical medicine, and oncology with considerable experience in both academe and industry. This leadership transition was made with the approval of our federal funding agencies and in consultation with our host academic institutions, Rutgers, The State University of New Jersey and the University of California, San Diego. Burley joined Rutgers in January 2013 to become Director of the Center for Integrative Proteomics Research, Director of the BioMaPS Institute for Quantitative Biology, a Distinguished Professor of Chemistry and Chemical Biology, and a Member of the Cancer Institute of New Jersey. He led RCSB PDB outreach efforts as an Associate Director, and assumed leadership of the RCSB PDB team at UCSD earlier this year when Phil Bourne became Associate Director for Data Science at the National Institutes of Health.

Dr. Helen M. Berman has led the RCSB PDB since 1998, and will continue her more than four-decade involvement with the Protein Data Bank (PDB) in her new role as Associate Director. Her focus will be on External Partnerships and activities related to hybrid or integrative structure determination methods. Berman, a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers, will also continue her leadership roles in the Nucleic Acid Database, the Structural Biology Knowledgebase, and the EMDataBank.

Berman and Burley are committed to an orderly transition to ensure our users uninterrupted access to high quality services providing a structural view of biology.

08-Jul-2014

Summer Newsletter Published

The Summer 2014 issue of the RCSB PDB Newsletter is now available.

PDB Reaches a New Milestone of 100,000+ Entries; the new wwPDB Deposition & Annotation System; RCSB PDB Mobile; a new Molecular Machinery poster; and more.

This issue's Education Corner highlights the results of our High School Video Challenge.

RCSB PDB's Newsletter is published online.  Sign up to receive electronic updates each quarter.

Past issues of the newsletter are available.

01-Jul-2014

Quick Tour of Search Results

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

24-Jun-2014

Depositing Data? Use the wwPDB Deposition & Annotation System

The new wwPDB Deposition & Annotation system is open for X-ray crystallographic structure depositions at deposit.wwpdb.org/deposition

Features of the new system include:

  • New data format: Extensible, dictionary-driven PDBx/mmCIF produces more uniform data across the archive
  • Deposition efficiency: ability to replace coordinate and/or experimental data files pre- and post- submission
  • Enhanced communication: 'In context' correspondence with wwPDB annotators and ability to preview and download processed files post-submission
  • Improved annotation: Improved ligand chemistry and polymer sequence checks with visual inspection provided during deposition
  • Validation: Geometry and experimental data checking during deposition and annotation is based on Task Force expert recommendations

17-Jun-2014

HIV Video Challenge Awards

The RCSB PDB recently challenged high school students to create short videos that tell a story about HIV/AIDS. Our judges were impressed by the science and storytelling techniques shown in the 23 videos submitted online.

2014 Video Challenge Awards


Judge's Award

Our panel of expert judges scored the videos based on scientific content (40%), creativity (20%), overall impact (10%), originality of concept (10%), entertainment value (10%), and production quality (10%).

  • First Place: The Lifecycle of HIV
    By John Quinlan, Kim Parker, Lisa Pullockaran of Hopewell Valley Central High School (Team Advisor: Karen Lucci)



  • Second Place: HIV: A Cellular Hijacker
    By Oneida Shushe of Colonie Central High School (Team Advisor: Jason Goldberg)



  • Third Place: HIV and Cancer
    By Pragnya Iyengar, Angela Gao, Shaina Brahma, Aashna Chopra of West Windsor-Plainsboro High School South (Team Advisor: Cindy Jaworsky)



Many thanks to our expert scientists: Gail Arnold (Rutgers University), Paul Craig (Rochester Institute of Technology), Kalyan Das (Rutgers University), Sunanda Gaur (Robert Wood Johnson Medical School), Graham Johnson (University of California San Francisco), Amisha Malhotra (Robert Wood Johnson Medical School), James Oleske (Rutgers New Jersey Medical School), and Art Olson (The Scripps Research Institute).


Viewer's Choice Award

Website visitors selected the same video as the judges: The Lifecycle of HIV by John Quinlan, Kim Parker, Lisa Pullockaran of Hopewell Valley Central High School (Team Advisor: Karen Lucci)


Service to the Community Award

The AIDS Education Training Center (AETC) National Resource Center was looking for possible training materials health care professionals, patients and their families, and selected the Judge's Second Place: HIV: A Cellular Hijacker By Oneida Shushe of Colonie Central High School (Team Advisor: Jason Goldberg)

Many thanks to all of the students, teachers, parents, judges, and voters who made this exciting competition happen! All of the submitted videos can be viewed online.

The resources created in support of this event (suggested resources, tutorials on making videos, and more) will continue to be hosted at PDB-101.

10-Jun-2014

Poster Prize Awarded at ACA

At the American Crystallographic Association's Annual Meeting (May 24-28, Albuquerque, NM), the RCSB PDB Poster Prize was awarded to Kimberly Stanek for
Crystal structure and functional characterization of an Hfq homolog from Aquifex aeolicus (Kimberly Stanek, Jennifer Patterson, Peter Randolph, Cameron Mura; University of Virginia)

Many thanks to judges Esko Oksanen (European Spallation Source) and  Michael Sawaya (UCLA), and to Marcia Colquhoun and the ACA.

All 2014 awardees will be listed on the RCSB PDB website and will receive an educational book.

The RCSB PDB also participated in several other events at the ACA meeting; pictures are online.

10-Jun-2014

Papers Published

One paper investigates how protein symmetry is linked to function and evolutionary processes, while another describes improvements made in the representation of peptide-like inhibitor and antibiotic molecules in the PDB.

  • Systematic Detection of Internal Symmetry in Proteins Using CE-Symm (2014) Journal of Molecular Biology 426: 2255-2268 doi: 10.1016/j.jmb.2014.03.010
  • Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank (2014) Biopolymers 101:659-668 doi: 10.1002/bip.22434

03-Jun-2014

Vote Now!

The RCSB PDB challenged high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS in a new competition.

View the videos online, and then cast your vote for the Viewer's Choice Award.

27-May-2014

RCSB PDB Mobile for iOS and Android

RCSB PDB Mobile is a universal app that enables the general public, researchers and scholars to search the PDB and visualize protein structures over a WiFi or cellular data connection.

Freely available for the iPhone/iPod/iPad and Android (2.3.3 and above), RCSB PDB Mobile can be used to search the entire PDB database, view the latest released structures, access  MyPDB accounts, and view the entire catalog of Molecule of the Month articles.

Interactive 3D visualization utilizes the program NDKMol (courtesy of Dr. Takanori Nakane, Kyoto University). Interactively view a molecule from by entering a PDB ID or launching the viewer from the search results. These views can be saved as images.

Different views are available. By default, the viewer displays macromolecules as ribbons, and small molecules as sticks.  These settings can be changed (using the "more" option on Android and "settings" on iOS) to highlight different features, with options to change:

  • Style of proteins, nucleic acids, and ligands
  • Ribbon color
  • Views of asymmetric unit, biological assembly, and crystal packing

RCSB PDB Mobile can be downloaded from the Apple Store and Google play.



Changing display options on iOS



Changing display options on Android

20-May-2014

Special Events in Albuquerque at ACA 2014

From May 24-28, the RCSB PDB will be at the 2014 Meeting of the American Crystallographic Association (ACA) in Albuquerque, New Mexico.  Many activities will highlight features of the new wwPDB Deposition and Annotation System.

Win door prizes and more at these special events:

  • Demonstration and Q&A.

Learn about the new features and enhancements of the new (and in production) wwPDB Deposition and Annotation System. Door prizes to be awarded! This event will take place Sunday, May 25 at 5pm in the Mesilla Room (one level above the exhibit hall and main session rooms, near the speaker ready room).

  • Helen Berman presents Databases in Crystallography: Past, Present, and Future as part of the Transactions Symposium: 100 Years of Crystallography session on Sunday.
  • Exhibition booth 212: Take the Depositor Survey about submission tools, Ask an Annotator your questions, and more.
  • Jasmine Young will present the New wwPDB Deposition and Annotation System as part of the Sunday poster session.
  • The RCSB PDB Poster Prize will be awarded to recognize a student poster presentation involving macromolecular crystallography.

The RCSB PDB will also be building virus and DNA models at the New Mexico Museum of Natural History & Science on Saturday alongside the ACA's workshop for high school teachers Crystallography: World of Wonders and the lunchtime lecture M.C. Escher and Crystallography presented by Dr. Doris Schattschneider.

Door prizes at the Sunday Q&A session include an autographed copy of David S. Goodsell's book The Machinery of Life; a copy of the original, out-of-print 2002 poster Molecular Machinery: Tour of the Protein Data Bank; and a printed copy of the new 2014 poster Molecular Machinery: Tour of the Protein Data Bank

Download the Calendar of Events

20-May-2014

Art of Science Travels to Paris, France

A new and improved version of the RCSB PDB's exhibit will be on display in Paris, France at the end of May.   The Art of Science uses the context of an art exhibit to introduce audiences new and old to to the beauty of the biomacromolecular structures and biology available in the PDB.

The two shows will be open to the public:

Since its beginnings in an art gallery at Rutgers University, the show has been hosted around the world  including Texas A&M University, EMBL-Hamburg, Germany; University of Wisconsin-Madison; California State University, Fullerton; Purdue University; and Hyderabad, India. The exhibit toured mostly between 2002-2007, with a recent iteration in Egypt in 2013.

The current exhibit includes images from the original Art of Science show along with new works inspired by important Molecule of the Month topics, molecular artist Irving Geis, and the International Year of Crystallography.

This event is curated by Christine Zardecki and Maria Voigt (RCSB PDB) and coordinated by Julien Muzard (Conservatoire National des Arts et Metiers).  Please contact Dr. Muzard with any local questions.

Upcoming events for the Art of Science are scheduled for the end of 2014 at McPherson College in Kansas and at the Delbarton School in New Jersey.  For additional details, please contact info@rcsb.org.

The Art of Science includes new works inspired by important Molecule of the Month topics, molecular artist Irving Geis, and the International Year of Crystallography.

The RCSB PDB team at Rutgers hosted a pop-up exhibit of the Art of Science before it was sent to Paris, France.

13-May-2014

PDB Reaches 100,000

With this week's update, PDB holdings now contain more than 100,000 current experimental entries. Visit the wwPDB to learn more about this significant milestone.

Download this image and add the number of structures deposited.

13-May-2014

Molecular Machinery Update

In 2002, Molecular Machinery: A Tour of the Protein Data Bank was published by the RCSB PDB.  Created by Molecule of the Month author David S. Goodsell, this illustration features 75 select structures from the PDB, showing their relative sizes at a scale of three million to one, and generally describes their critical roles in the functions of living cells.  The image, available as a poster and handout, has been distributed to thousands of PDB users, teachers, and students over the years.

In celebration of the release of more than 100,000 structures in the PDB archive, Goodsell and RCSB PDB have updated this iconic image in a new Tour of the Protein Data Bank.

The 2014 poster uses 96 structures to illustrate the vast range of molecular shapes and sizes in the PDB.  The structures are depicted relative to the cellular membrane and organized in categories related to function.  A scale bar provides a sense of molecular size in nanometers.

The poster (PDF) is 34 x 22" and 23MB, and the double-sided flyer (PDF) is 8 1/2 x 11". Both the 2002 and 2014 posters will be available for download from PDB-101.

Copies of the 2002 and 2014 posters will be part of a raffle at the upcoming ACA meeting.  Visit the RCSB PDB booth in the exhibit hall at the meeting to learn more!

Original 2002 poster

2014 Tour of the Protein Data Bank

06-May-2014

Video Challenge for High School Students

The RCSB PDB invites high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS in a new competition. The video must include a visualization/animation of two or more molecular structures from the PDB and may be focused on any topic related to the structural biology of HIV/AIDS. Videos will be considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community. The deadline for submission is May 31, 2014.

Visit PDB-101 for an overview, rules, suggested resources, tutorials on making videos, and more.

29-Apr-2014

New Website Release

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

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

A Validation Report slider gives an indication of the quality of the determined structure.

22-Apr-2014

Visit the USA Science and Engineering Festival Expo on April 26 & 27

The USA Science & Engineering Festival is a national grassroots effort to advance STEM education and inspire the next generation of scientists and engineers.  The festival's Expo will take over the entire Walter E. Washington Convention Center in Washington, DC. with more than 3000 fun, hands-on activities for all ages, and stage shows featuring music, magic, comedy and more on April 26 & 27.

At booth #616 in Hall A, the RCSB PDB will host hands-on DNA and virus building to promote a structural view of biology. RCSB PDB will participate in Sneak Peek Friday.  The booth will also be part of the Evolution Thought Trail sponsored by the Society for Developmental Biology--visit 3 booths on the trail and win a prize!

Can't make it to Washington, DC?  Build models at home of DNA, dengue virus, and more using resources from PDB-101

22-Apr-2014

DNA Day 2014: 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:

Build PDB-101's paper model of DNA

15-Apr-2014

Resources for High School Video Challenge

The RCSB PDB invites high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS in a new competition. Videos must include a visualization/animation of two or more molecular structures from the PDB and may be focused on any topic related to the structural biology of HIV/AIDS.

Submitted videos will be reviewed by an expert panel and considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community.

New online video tutorials are available to help students interested in creating molecular animations for their videos. Tutorial 1 demonstrates Protein Visualization with UCSF Chimera, Video Editing with Blender, and Sound Editing in Audacity. Tutorial 2 describes Finding and visualizing HIV-related protein-drug complexes.

Other resources, including a paper model of the HIV capsid and related Molecule of the Month columns on HIV capsid, HIV-1 protease, Integrase, Reverse Transcriptase, HIV Envelope Glycoprotein, and Broadly Neutralizing Antibodies, are available from PDB-101 for use in any video.

Visit PDB-101 for an overview, rules, related resources, and more. Sign up for the Video Sign up for the Video Challenge Newsletter for regular updates and suggestions.

The deadline to submit a video is May 31, 2014.

Spread the news! A PDF flyer describing this challenge is available for download and distribution.

RCSB PDB HIV video challenge

08-Apr-2014

Spring Newsletter Published

The Spring 2014 issue of the RCSB PDB Newsletter is now available.

Read about the High School Video Challenge, the new wwPDB Deposition and Annotation system, search options for finding membrane proteins, and more.

This issue's Education Corner describes The Virtual Drug Screening Stream: research and discovery as undergraduates at UT Austin.

RCSB PDB's Newsletter is published online. Sign up to receive electronic updates each quarter.

Past issues of the newsletter are available online.

01-Apr-2014

Build a Model of GFP

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 include a PDF that can be used to create a 3D model of Green Fluorescent Protein and a related Activity Page that includes background information on GFP, a video demonstrating how to create the GFP model, and a curated interactive molecular view.

Other GFP resources include the Molecule of the Month article and a Bioinformatics of Green Fluorescent Protein tutorial guide.


01-Apr-2014

Our Best Wishes to Phil

After serving as Associate Director of the RCSB PDB, Philip E. Bourne has now taken on the role of Associate Director for Data Science at the NIH.  Phil was part of the original team that brought the management of the PDB to the RCSB in 1998. From database development, literature integration, and visualization tools, Phil's influence is felt in every aspect of the resource used by hundreds and thousands of RCSB PDB users from around the world.

The entire RCSB PDB team thanks Phil and wishes him the best of luck in his new adventures in the world of 'Big Data' management.

25-Mar-2014

Learn How to Create Molecular Animations

The RCSB PDB's new Video Challenge invites high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS.

New online video tutorials are available to help students interested in creating molecular animations for their videos.

Tutorial 1 demonstrates Protein Visualization with UCSF Chimera, Video Editing with Blender, and Sound Editing in Audacity. Tutorial 2 describes Finding and visualizing HIV-related protein-drug complexes.

Other resources, including a paper model of the HIV capsid and related Molecule of the Month columns, are available from PDB-101 and can be used in videos that do not involve molecular animations.

The deadline to submit a video is May 31, 2014.

25-Mar-2014

The Art of Systems Biology and Nanoscience

Molecule of the Month author and illustrator David S. Goodsell will be part of a special multidisciplinary look into the world of living cells. The Art of Systems Biology and Nanoscience will take place March 28 - 29, 2014 at the 333 Montezuma Arts gallery in Sante Fe, NM with presentations, art exhibits, and performances that explore molecular pathways and cellular structures.

The Art of Systems Biology and Nanoscience is an annual event.

Painting of an entire Mycoplasma mycoides cell by David S. Goodsell, the Scripps Research Institute.

18-Mar-2014

Visit the San Diego Festival of Science and Engineering on March 22

On Saturday March 22, 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 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.

11-Mar-2014

Author Profiles: Timeline Display of a Researcher's Structures

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.

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

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

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

11-Mar-2014

Meet the RCSB PDB Team



The RCSB PDB was able to participate virtually at this year's Biophysical Society meeting through Biophysical Society TV. This video, which was aired at the meeting, highlights some of RCSB PDB's efforts in data annotation and in education.  The full channel hosts interviews filmed at the meeting (including an interview with Jane Richardson (Duke) on Celebrating 100 Years of Crystallography) and features on other resources (including the New York Structural Biology Center).

04-Mar-2014

Membrane Query and Annotation

Users can quickly find all annotated membrane proteins in the PDB by entering "membrane proteins" in the top bar simple search and selecting the "Retrieve Membrane Proteins" option.

The Membrane Protein Browser and the Membrane Proteins drill-down tool from the home page and search results can be used to investigate specific membrane protein classifications and access the corresponding structures.

Membrane protein annotations for each entry appear in the Search Results and individual Structure Summary pages (example: 2rh1).

Transmembrane proteins in the PDB are identified using the mpstruc database (Stephen White, UC Irvine), sequence clustering, and data derived from UniProt. Details are available.

Explore Membrane Protein Classifications using the drill-down tool from the home page (shown) or search results.

Explore Membrane Protein Classifications using the drill-down tool from the home page (shown) or search results.

25-Feb-2014

Video Challenge for High School Students

The RCSB PDB invites high school students to create short videos (two minutes or less) that tell a story about HIV/AIDS in a new competition. The video must include a visualization/animation of two or more molecular structures from the PDB and may be focused on any topic related to the structural biology of HIV/AIDS.  Videos will be considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community.  The deadline for submission is May 31, 2014.

Visit PDB-101 for an overview, rules, suggested resources, tutorials on making videos, and more.

18-Feb-2014

Releasing Structures on Hold for Publication

Of all PDB entries deposited in 2013, 83.7% were submitted with a release status of "hold until publication (HPUB)"; 13.7% were released as soon as annotation of the entry was complete; and 2.6% were held until a particular date.

For structures with HPUB status, entries will be released as part of the weekly update upon confirmation the corresponding article has been published.

The wwPDB receives publication dates and citation information directly from a few journals (see the wwPDB's Information for Journals). For most articles, however, the wwPDB searches PubMed  and scans  the literature for publication information. Citations emailed to deposit@wwpdb.org are also greatly appreciated.

There is a one-year limit on the length of a hold period, including HPUBs. If the citation for a structure is not published within the one-year period, depositors will be given the option to either release or withdraw the deposition.

11-Feb-2014

Find PDB Structures with Protein Purification Tags

Protein tags are peptide sequences attached to proteins for various experimental reasons, particularly for purification.   Advanced Search can be used to search for entries with these protein purification tags.

To find these structures, select the Sequence Features > Sequence Motif option and enter an exact sequence or a sequence pattern expressed by regular expression syntax. Regular expressions can be used to define complex sequence patterns.

Entering ^HHHHHH will search for a 6 residue long N-terminal polyhistidine-tag (His6 tag), while a search for HHHHHH will find any sequence with a (His)6 pattern. This query looks at the sequence originally studied, and will find entries where an His6 tag appears completely, in part, or not at all in the coordinates.

More details about the sequence motif search are available.

Entry 4bnx contains a His6 tag

Entry 4bnx contains a His6 tag

04-Feb-2014

Tour of Ligand Deposition

As announced by the wwPDB, a new deposition system for structures determined using X-ray crystallography has been launched. New or enhanced features of this system include the generation of X-ray validation reports (following the recommendations of the wwPDB X-ray Validation Task Force), improved capture and review of ligand information, the ability to replace coordinate and/or experimental data files pre- and post-submission, improved communication process between depositors and wwPDB curators, and the ability to preview and download the PDBx/mmCIF entry file prior to submission.

New videos demonstrate how to review and submit ligands in this new system.   

For all ligands present in the uploaded coordinate file, the deposition system will search for graphical matches against all released ligands in the PDB. Close (but not exact) matches will require depositor attention as demonstrated here:



When the system cannot find a match for a ligand, depositors will be required to provide a SMILES or InChI string or a 2D chemical drawing, as shown in this video:

Depositors will have the option to use the new system or one of the legacy deposition tools (ADIT, AutoDep) for most of 2014. After the transition to the new system, the legacy tools will be available for a limited period of time to complete any unfinished deposition sessions.

In the interest of a smooth transition, the number of X-ray structures that will be processed by the new system will increase gradually over the next few months. After this period, it will also become possible to deposit NMR and 3DEM structures with the new system.

Up-to-date information about the new system, tutorials for getting started, and an FAQ are available from the wwPDB website.

28-Jan-2014

Binding Site Visualization

Options for visualizing binding sites have been added to the Jmol options available at rcsb.org.

From a Structure Summary page (example: 1stp), select the option for "3D View" listed under the entry's image (or from the 3D View tab).

Options for viewing domains and ligands are at the bottom of the page.

Select the Ligand tab and then the link to "View Pocket in Jmol" to access this new feature.  Residues are displayed in contact with the selected ligand. A cropped ligand van der Waals surface will appear that is color coded by the proximity to the van der Waals surface of the binding site (red: close contact, blue: far contact).

Thanks to Robert Hanson (St. Olaf College), the current principal Jmol developer, for implementing this feature during his visit to the RCSB PDB.

The biotin binding site in PDB entry 1stp.  To access this view, select the 'Ligands' tab and click on 'View Pocket in Jmol'.

The biotin binding site in PDB entry 1stp. To access this view, select the 'Ligands' tab and click on 'View Pocket in Jmol'.

21-Jan-2014

Big Picture on Proteins

The Wellcome Trust produces a free educational resource, Big Picture, for biology students and their teachers.

The latest issue is focused on proteins, and utilizes images from RCSB PDB's Molecule of the Month.

Available resources include a print magazine and an online collection of related materials, including:

Visit www.wellcome.ac.uk/bigpicture/proteins for these resources and more.

For additional educational materials about proteins and nucleic acids, visit the RCSB PDB's website PDB-101.

Visit www.wellcome.ac.uk/bigpicture/proteins for the Big Picture issue focused on proteins and related materials.

Visit www.wellcome.ac.uk/bigpicture/proteins for the Big Picture issue focused on proteins and related materials.

14-Jan-2014

Teacher Workshop in Boulder, Colorado

Register Colorado Workshop

Join the RCSB PDB and the Colorado Biology Teachers Association for an Introduction to Protein Structure and Function: the RCSB PDB as a teaching resource.

This workshop will take place on Saturday, January 25, 2014 at Fairview High School in Boulder, CO. 0.5 Adams State College graduate credits available for additional fee.

Register at www.cbtapdb.eventbrite.com.

14-Jan-2014

RapiData 2014

As part of RapiData 2013, RCSB PDB's Peter Rose visited the new National Synchrotron Light Source II at BNL

As part of RapiData 2013, RCSB PDB's Peter Rose visited the new National Synchrotron Light Source II at BNL.

Synchrotron radiation has become an indispensable tool for many macromolecular crystallography groups. Some synchrotron-specific skills are difficult to learn without ones having an intensive hands-on training program. But not all research groups have the luxury of providing long training sessions for students and postdocs. To provide such an educational experience, RapiData Collection & Structure Solving is a practice course in Macromolecular X-ray Diffraction Measurement.

RapiData will take place April 27-May 2, 2014 at Brookhaven National Laboratory. Information and registration is available at www.bnl.gov/rapidata.

07-Jan-2014

Winter Newsletter Published

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

Read about the PDB and the International Year of Crystallography, data deposition and website statistics for all of 2013, searches by gene name and transporter classification, the RCSB PDB's 2013 Annual Report, and more.

The Education Corner describes at a new video challenge for high school students.

RCSB PDB's Newsletter is published online.  Sign up to receive electronic updates each quarter.

Past issues of the newsletter are available online.