PROCHECK protocols

View PROCHECK computational protocol

PROCHECK statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Structure validation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

Maintainer


  • person_outline Roman Laskowski <>

Additional information


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

Publications for PROCHECK

PROCHECK in pipelines

 (106)
2018
PMCID: 5855608
PMID: 29382080
DOI: 10.3390/ijms19020386

[…] measured by the z-score; the difference between the average and raw scores in the unit of standard deviation []., the stereochemical quality of the generated model was checked using a program called procheck []. it verifies the quality of model by computing several parameters such as side chain conformations of protein structures as a function of atomic resolution, lengths, geometry […]

2018
PMCID: 5880399
PMID: 29608608
DOI: 10.1371/journal.pone.0195355

[…] the 2d secondary structure prediction of pgds was performed using psipred server [], and the 3d model was generated by swiss-model[]. the structure validation and quality control was done by procheck [] and whatcheck module on whatif server []., pgds activity was assayed using γ-pga as the substrate. γ-pga were reagent grade and purchased from sigma-aldrich. γ-pga (100ug) was incubated […]

2018
PMCID: 5902840
PMID: 29661206
DOI: 10.1186/s13104-018-3354-1

[…] template for structural modeling was identified using pdb-blast. protein model was developed using swiss-model (https://swissmodel.expasy.org/) [–] and verified with ramachandran plot, procheck analysis, global model quality estimation (gmqe) score and qualitative model energy analysis (qmean) values []., the structures of wa, mtx and dhfa (pubchem cid 265237, 126941, 98792, […]

2017
PMCID: 5320522
PMID: 28225045
DOI: 10.1038/srep43043

[…] to protein data bank (pdb) format. the protein structure validation suite (http://psvs-1_5-dev.nesg.org/) was used to obtain statistics for the twenty lowest energy structures of tirap pbm. by using procheck, the ramachandran analysis of the twenty lowest-energy conformers of tirap pbm identified that 97.5% of the residues are in the most favored regions, 2.5% in the additionally allowed […]

2017
PMCID: 5405553
PMID: 28446174
DOI: 10.1186/s12918-017-0427-z

[…] [] (http://robetta.bakerlab.org) except for rpsl (homology modeling was used) and the models generated were checked for various parameters for model assessment, such as ramachandran plots using procheck. finally, visualization and manipulation of the three dimensional models were performed using the software pymol (schrödinger, llc, 2015). in addition 3dligandsite [] was used to get […]


To access a full list of citations, you will need to upgrade to our premium service.

PROCHECK in publications

 (2125)
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 […]

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 [, ]. […]

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 […]

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 […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

PROCHECK reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PROCHECK