RCSB PDB Help

Structure Validation and Quality

Access additional resources of interest, submitted by community members.

CheckMyMetal	A service checks metal binding site and validation
MolProbity	Structure validation on client-uploaded or PDB ID-specified files, using all-atom contact analysis tools and updated geometrical criteria for phi/psi, sidechain rotamer, and Cbeta deviation
NQ-Flipper	NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures obtained from X-ray crystallography, NMR or modelling studies.
Procheck	A program that checks the stereochemical quality of a protein structure
Prosa-web	Quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer.
Verify3D Structure Evaluation Server	Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures.
WHAT IF	A protein structure analysis program that may be used for mutant prediction, structure verification and molecular graphics
WHAT_CHECK	A system for protein structure validation derived from the WHAT IF program

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Last updated: 2/23/2023

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.