PROCHECK statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PROCHECK
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Tool usage distribution map

This map represents all the scientific publications referring to PROCHECK per scientific context
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Associated diseases

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Protocols

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

[…] ing in favoured, unfavoured or disallowed regions, the number of glycine and proline residues and orientation of their backbone dihedral angles including the phi (φ) and psi (ψ) angles with using the PROCHECK module of the PDBsum server http://www.ebi.ac.uk/pdbsum/ []. Furthermore, qualitative assessment measured in terms of stability and reliability of the predicted models was evaluated through t […]

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

[…] generated were subjected to energy minimization using the “steepest descent” technique to eliminate bad contacts between protein atoms. Stereo-chemical quality of minimized models was analyzed, using procheck tool (Laskowski et al., ). […]

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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