Exploring Structure Quality

02/24

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:

• A PDF report containing Ramachandran plots created using MolProbity. 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.
• 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)

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 1cbs as created by MolProbity.

News Index

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• 12/22 Poster Prize Awarded at AsCA

• 12/15 Smart Searching

• 12/08 Tour of Ligand Deposition

• 12/01 Validate Before Depositing to Save Time

• 11/24 Advanced Search: Multiple ID Search

• 11/17 Comparison Tool for Exploring Sequence and Structure Alignments

• 11/10 Visualize Structure Quality and Mutations with Protein Feature View

• 11/03 Structure Summary Pages Redesigned

• 10/27 Upcoming Meeting: SACNAS

• 10/20 Molecular Origami: Insulin

• 10/13 Fall Newsletter Published

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• 09/29 Poster Prize Awarded at ISMB/ECCB

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• 09/15 RCSB PDB Software Shared on GitHub

• 09/08 Head Back to School with PDB-101

• 09/01 Poster Prize Awarded at ACA

• 08/25 Annual Report Published

• 08/18 Take an Interactive Tour of the Protein Data Bank

• 08/11 Save References to Mendeley and Endnote

• 08/04 Explore PDB Structures by Browsing Annotations

• 07/28 Web Services for Accessing PDB Data

• 07/21 Summer Newsletter Published

• 07/14 Membrane Query and Annotation

• 07/07 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 07/07 Poster Prize Awarded at ICSG

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• 06/23 Map Genomic Position to Protein Sequence and Structure

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• 04/21 DNA Day 2015: April 25

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• 04/14 Education Corner: The Science of HIV

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• 03/31 Take an Interactive Tour of the Protein Data Bank

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• 03/17 Visit the San Diego Festival of Science and Engineering on March 22

• 03/10 2015 High School Video Challenge

• 03/03 New Publications

• 03/03 San Diego Science Olympiad Protein Modeling Results

• 02/24 Exploring Structure Quality

• 02/17 2015 High School Video Challenge Materials

• 02/10 BioJava 4.0.0 Released

• 02/03 NJ Science Olympiad Protein Modeling Results

• 01/27 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 01/20 RCSB PDB Mobile for iOS and Android Update

• 01/13 Winter Newsletter Published

• 01/06 Video Challenge for High School Students

• 01/06 New Calendar Celebrates 15th Anniversary of Molecule of the Month