Explore PDB Data Overviews

09/25

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PDB Data  Overviews.

The RCSB PDB maintains several lists that display PDB data in interesting and useful ways. Highlights include:

• Proteins Solved by Multiple Experimental Methods

This page lists clusters of proteins (with greater than 95% sequence similarity) containing at least one structure solved by one method (e.g. X-ray) and one by a different method (e.g. NMR).

• PDB Statistics: Content Distribution & Growth

View histograms of the PDB archive based on characteristics like space group, journal, Enzyme Classification, and more. The growth of the number of PDB entries released per year is organized around experimental method, molecule type, and unique protein classifications. Data can be downloaded as Excel documents.

• RSS Feeds

Subscribe to RSS feeds to access the latest structures (from the RCSB PDB) and Molecule of the Month articles (from PDB-101) as soon as they become available.

• Summaries of PDB Data

Links to summary files available from the PDB FTP, including a file with all PDB sequences in FASTA format; one with all PDB IDs, molecule type, and experimental method; and one with all PDB IDs and authors.

• Secondary Structure Files

A FASTA formatted file generated using DSSP displays sequences and secondary structure for all entries. A separate file includes notation of regions which have not been experimentally observed in addition to the secondary structure.

• Latest weekly release and all released entries

The top right of every RCSB PDB page header links to the full archive (select the number of total structures) and to the entries in the most recent update (select the date listed).

• PDB-101: Author Profiles

Author Profiles vertically display structures associated with a particular researcher. Profiles are also available for Structural Genomics centers.

• PDB-101: Molecule of the Month

Articles are indexed by title, date, and category, and accessible from an alphabetical pull-down menu.

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

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• 11/13 Ligand Searching

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• 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

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• 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