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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

 (2142)
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

[…] in the present study, we focused on a 3-d structural model of gpr120 has been constructed using homology modeling techniques. the structural quality of the predicted gpr120 model was verified using procheck, whatif, prosa, and verify 3d. after this chemical database of natural compounds have been constructed and screened for its druggability using molinspiration server. molecular docking […]

library_books

Identification of a peptide inhibitor for the histone methyltransferase WHSC1

2018
PLoS One
PMCID: 5942779
PMID: 29742153
DOI: 10.1371/journal.pone.0197082

[…] - ‹i›|)/ σi ii], 2 rvalue = σhkl ||fobs|—|fcalc|| / σhkl |fobs|, rfree is the cross-validation r factor computed for the test set of 5% of unique reflections, 3 ramachandran statistics as defined by procheck, nsd family members are large, multi-domain containing enzymes that, in addition to the catalytic set domain, include known epigenetic reader domains such as phd and pwwp domains [, ]. […]

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

[…] 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 […]

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

[…] 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. ., proteins were purified and concentrated to 10 g l−1. crystallization […]

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

[…] 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 […]

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

[…] 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., )., to predict the effects of mutations on the stability of il10ra protein at three dimensional structure level, duet (pires et al., ), an integrated computational […]


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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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