Papers Published

12/18

Articles covering a variety of topics have been published:

• The RCSB Protein Data Bank: new resources for research and education (2013) Nucleic Acids Research doi: 10.1093/nar/gks1200

Update of new tools and resources that provide a structural view of biology for research and education, including improved methods for simple and complex searches of PDB data, creating specialized access to chemical component data and providing domain-based structural alignments.

• Creating a community resource for protein science (2012) Protein Science 21: 1587-1596 doi: 10.1002/pro.2154

Discusses how management, data content, infrastructure, and community have influenced the continued development of the PDB. It also analyzes the corpus of data to identify trends in the field of structural biology.

• BioJava: an open-source framework for bioinformatics in 2012 (2012) Bioinformatics 28: 2693-2695 doi:10.1093/bioinformatics/bts494

Describes modules that provide state-of-the-art tools for protein structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detection of protein modifications and prediction of disordered regions in proteins as well as parsers for common file formats using a biologically meaningful data model.

• Illustrating the Machinery of Life: Viruses (2012) Biochemistry and Molecular Biology Education 40: 291-296 doi: 10.1002/bmb.20636

David Goodsell's series continues with illustrations of poliovirus, influenza, and HIV.

• Putting proteins in context (2012) Bioessays 34:718-20 doi: 10.1002/bies.201200072

David Goodsell describes his thoughts and process for scientific illustrations.

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

News Index

• 12/25 Happy Holidays

• 12/18 Join the RCSB PDB Team

• 12/18 Papers Published

• 12/11 Announcement: Meeting on Hybrid Methods

• 12/11 Map PDB Structures to Full-length Protein Sequences

• 12/04 Advanced Search: Multiple ID Search

• 11/27 World AIDS Day: December 1

• 11/27 MyPDB: Keep up-to-date with new structures... automatically!

• 11/20 Educational Activities and Lessons

• 11/20 Take our quick survey

• 11/13 Take our quick survey

• 11/13 Ligand Searching

• 11/06 Explore Gallery View of Search Results

• 10/30 Improved Drug Searches and Annotations

• 10/23 New Website Release

• 10/16 Nobel Prize Awarded for studies of G-protein-coupled receptors

• 10/16 Explore the Structural Biology of HIV

• 10/09 Fall Newsletter Published

• 10/02 Advanced Search: Sequence Motif

• 10/02 Turn Your Computer into a PDB Structure Kiosk

• 09/25 Explore PDB Data Overviews

• 09/18 High Resolution Images at the RCSB PDB

• 09/11 Poster Prize Awarded at ECM

• 09/11 Customized Home Page: Structure Comparison Tool

• 09/04 Head Back to School with PDB-101

• 08/28 Smart Searching with the Top Bar Suggestion Box

• 08/21 Download RCSB PDB Mobile for the iPhone/iPad

• 08/21 Poster Prize Awarded at ACA

• 08/14 Poster Prize Awarded at ISMB

• 08/14 Improved Ligand Reports

• 08/07 Build complex queries with Advanced Search

• 07/31 Prepare data for deposition with pdb_extract and SF-Tool

• 07/31 Protein Society Annual Symposium

• 07/24 Upcoming Meeting: ACA

• 07/17 Different Ways To Explore New Entries

• 07/10 ISMB and 3DSIG Meetings

• 07/10 Summer Newsletter Published

• 07/03 Author Profiles: Timeline Display of a Researcher's Structures

• 06/26 Latest Website Release

• 06/19 Personalize the RCSB PDB with MyPDB

• 06/19 National Protein Modeling Champions

• 06/12 Top Bar SMILES String Searching

• 06/05 Molecule of the Month reaches 150

• 05/29 Tour the PDB with Drill-down Pie Charts

• 05/22 Domain-based Structural Alignments

• 05/15 New Poster: Virus Structures

• 05/08 Bookmark and Post Webpages

• 05/08 Customized Home Page: Sequence Search

• 05/01 Latest Website Release

• 04/24 Rutgers Day (April 28)

• 04/24 Create a Collage of Structures

• 04/17 DNA Day 2012: April 20

• 04/17 Exhibiting at Experimental Biology

• 04/10 Spring Newsletter Published

• 04/03 Depositing Structures with Ligands

• 03/27 Browse the PDB by GO Terms, EC Number, Source Organism, and More

• 03/20 Visit the San Diego Festival of Science and Engineering on March 24

• 03/20 J.P. Stevens HS Wins NJ Protein Modeling Event

• 03/13 Sound Science

• 03/13 PDBMobile and iOS 5.1

• 03/13 Preview New 3D Similarity Tab

• 03/06 Explore a Structural View of Biology at PDB-101

• 02/28 Visualize Molecular Surfaces with Protein Workshop

• 02/21 New Structures Widget

• 02/21 Visit the Biomolecular Discovery Dome at Biophysical Society

• 02/14 Ligand Summary Pages

• 02/07 Free Webinar and Updated Tutorial

• 02/07 Volunteer Structures For Foldit

• 01/31 Announcement: Meeting on Hybrid Methods

• 01/31 Free Webinar on How to use the RCSB PDB

• 01/24 Newsletter Published

• 01/17 NJ Science Olympiad Protein Modeling Results

• 01/10 Web Services for Accessing PDB Data

• 01/03 Annual Report Published