PROCHECK pipeline

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

 (42)
2017
PMCID: 5405553
PMID: 28446174
DOI: 10.1186/s12918-017-0427-z

[…] [27] (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 [28] was used to get […]

2017
PMCID: 5705324
PMID: 28993624
DOI: 10.1038/s41564-017-0041-2

[…] configuration based on their backbone chemical shifts and predictions using promega software43. the structure ensemble was visualized and inspected with pymol44 and the quality was evaluated with procheck-nmr45 and the psvs server46. the structure atomic coordinates and restraints used in the calculation were deposited in the protein data bank (pdb id: 5o2y). we estimated the global rotation […]

2017
PMCID: 5814841
PMID: 29294091
DOI: 10.1093/nar/gkx1275

[…] refinement was performed until no noe violations >0.2 å and no dihedral angle violations higher than 5° occurred. the restraint violations and structure quality were assessed using the cns tools, procheck-nmr (62) and in-house software and utilities. at the last iteration of the refinement protocol 100 structures have been calculated using 1577 unambiguous distance and 199 dihedral angle […]

2016
PMCID: 4789359
PMID: 27034663
DOI: 10.1155/2016/3136024

[…] followed by the validation of the 3-dimensional structure using saves (http://services.mbi.ucla.edu/saves/), where the stereochemical quality of the 3d model obtained was verified using a program procheck [42, 43] for the purpose of selecting the best model. verify 3d structure evaluation server [44, 45] was used for 3d-profiling of the residues, errat [35] for the verification of protein […]

2016
PMCID: 4839703
PMID: 27101008
DOI: 10.1371/journal.pone.0153868

[…] were improved by energy minimization using 200 cycles of the steepest descents and 500 cycles of the conjugate gradient. the stereochemical quality of the selected model was evaluated using the procheck program [28].thepymol molecular graphics system (delano scientific, san carlos, 184 ca. http://www.pymol.org.) was used in order to visualize the constructed model structures and to generate […]

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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