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PROCHECK specifications

Information


Unique identifier OMICS_06366
Name PROCHECK
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A file holding the coordinates of the structure of interest.
Input format PDB
Output data A number of plots, together with a detailed residue-by-residue listing.
Operating system Unix/Linux
Computer skills Advanced
Version 3.5
Stability Stable
Maintained Yes

Subtool


  • PROCHECK-NMR

Versioning


No version available

Maintainer


  • person_outline Roman Laskowski

Additional information


https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/manual/

Publications for PROCHECK

PROCHECK citations

 (2386)
library_books

A new insight into identification of in silico analysis of natural compounds targeting GPR120

2018
PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] hree-dimensional structure of GPR120 receptor through homology modeling using delta opioid 7tm receptor (PDB ID: 4N6H) as a template. The generated model was assessed by several validation tools like Procheck, Errat, whatif, ProSA 2007, and Verify 3D. All above-mentioned tools revealed that the model is reliable. This model was also submitted to PMDB server (PDB: PM0079568) for public assessment. […]

library_books

Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

2018
PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] l, RAMPAGE, ERRAT, ProSA and Verify3D software package were used. RAMPAGE is a branch of RAPPER that engender a Ramachandran plot. It's counselled that it's used for this principle in predilection to PROCHECK, which relies on a lot of huge information. The Ramachandran plots psi versus phi dihedral angles for every amino acid within the protein. The plot is split into favoured, approved and barred […]

library_books

Structures of chaperone substrate complexes docked onto the export gate in a type III secretion system

2018
Nat Commun
PMCID: 5932034
PMID: 29720631
DOI: 10.1038/s41467-018-04137-4

[…] t target function were subjected to restrained molecular dynamics energy water refinement using CNS. The percentage of residues falling in favored and disallowed regions of the Ramachandran plot from Procheck is: 99.7% and 0.3%, respectively. The ensemble of the 15 lowest-energy conformers are shown in Supplementary Fig. . […]

library_books

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

2018
PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] trast, the selected protein model SolyWRKY37 had 98.3% (favoured) and 1.7% residues lying in the additionally allowed segments. However, the qualitative assessment through PDB sum server and based on PROCHECK analysis we found that 96.3% residues in most favoured, 3.7% additionally allowed and 0.0% in the generously allowed regions and 0.0% in the disallowed regions (XX) with the G factor values ( […]

library_books

Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

2018
Front Genet
PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] After the energy minimization of 3D models, stereochemical quality of the structures was validated by PROCHECK server. The results of the PROCHECK analysis indicated that a relatively low percentage of residues have phi/psi angles in the disallowed regions suggesting the acceptability of Ramachandran […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] nding structure models were selected for subsequent analysis. Further the selected protein structure models were checked for their quality using Verify3D (http://servicesn.mbi.ucla.edu/Verify3D/) and PROCHECK (http://servicesn.mbi.ucla.edu/PROCHECK/) (Supplementary Table ). Thus, good quality structure models of filtered proteins in A. fumigatus Af293 were compared to the structure of their corres […]

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PROCHECK institution(s)
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, London, UK; Crystallography Department, Birkbeck College, London, UK

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