Model Validation

This section includes a number of web tools and databases that may help in assessing the reliability of structural models (crystallographic, NMR, or homology based models).

open in new windowEDS Electron Density Server - a collection of reports on models from the PDB (for which experimental crystallographic data has been deposited) with a focus on the fit of the model to the data
open in new windowPDBREPORT database of automatically made WHAT CHECK reports for all PDB entries
open in new windowPDBsum Each entry Includes links to PROCHECK, WHAT CHECK and EDS reports
open in new windowERRAT Uses to analyze the statistics of non-bonded interactions between different atom types.
Eval123D Performs the quality checks provided by the programs Verify3D, Eval23D ProSA and EvTree.
open in new windowJCSG Structure Validation Central Performs any or all of the quality checks provided by the programs PROCHECK, SFCHECK, PROVE, ERRAT, WASP, DDQ, WHAT CHECK and PSQS.
open in new windowMetaMQAPII Metaserver for quality assessment of protein structures optimized for theoretical models
open in new windowMolProbity Includes steric and geometric analyses.
open in new windowPARVATI Analysis tool for macromolecular structure refinements that include anisotropic displacement parameters.
open in new windowpdb-care Carbohydrate residue checks.
open in new windowProSA Fold reliability analysis.
open in new windowPSVS Performs the quality checks provided by the programs PROCHECK, Verify3D, MolProbity ProSA and more.
open in new windowRamachandran plot Ramachandran plot analysis.
open in new windowRAMPAGE Ramachandran plot analysis.
open in new windowSTAN the STructure ANalysis server, performs the quality checks provided by the programs WASP, CISPEP and MOLEMAN2
open in new windowVADAR

Volume, Area, Dihedral Angle Reporter. Includes excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality.

open in new windowVerify3D Assessment of protein models with 3-D sequence profiles.
Programs that Incorporated in the Servers
open in new windowCISPEP
Uses to investigate if any non-proline peptide bond that has been modeled as trans could in reality be cis.
Difference density quality analysis.
open in new windowMOLEMAN2
Includes geometry and dihedrals angles analyses.
open in new windowPROCHECK
Includes stereochemical quality checks.
Atomic volume check.
open in new windowSFCHECK
A program for assessing the agreement between the atomic model and X-ray data or EM map.
Uses to investigate if certain water molecules could be metal ions instead.
open in new windowWHAT CHECK
A protein verification tools from the open in new windowWHAT-IF program. Includes stereochemical, steric, nomenclature, and packing quality checks. The checks can be accessed via open in new windowWHAT-IF servers (Build/check/repair model server).