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PROSESS specifications

Information


Unique identifier OMICS_17111
Name PROSESS
Alternative name Protein Structure Evaluation Suite & Server
Interface Web user interface
Restrictions to use None
Input data A 3D protein model, a primary sequence in if the 3D model has missing residues, distance restraints with residue numbers matching the 3D model (optional) and chemical shifts in with residue numbers matching the 3D model (Optional).
Input format PDB, fasta, XPLOR, and BMRB NMR-STAR 2.1 or NEF
Output data Four "clickable" pages: Global Structure Assessment, Local (Per-residue) Structure Assessment, Graphs and Figures and Similarity Assessment.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline David Wishart <>

Additional information


http://www.prosess.ca/i_o_formats.html; http://www.prosess.ca/output_formats.html

Publication for Protein Structure Evaluation Suite & Server

PROSESS in publications

 (5)
PMCID: 5596018
PMID: 28900197
DOI: 10.1038/s41598-017-11736-6

[…] set to 10 with a step size of 0.02 å. the secondary structure of the modeled protein was validated using protein structure validation suite (psvs) and protein structure evaluation suite and server (prosess). the secondary structure elements of the 3d model were compared with those of the predicted ones in order to measure the structural reliability. the selected p4a model was subjected to md […]

PMCID: 4299175
PMID: 25519881
DOI: 10.1186/s12858-014-0027-0

[…] in our hybrid model was further ascertained by the structure analysis and verification server v4 (saves, see http://services.mbi.ucla.edu) and protein structure evaluation suite and server (prosess, see http://www.prosess.ca/) [], and details of the analysis are compiled in additional file : figure s5., the molecular dynamics simulations were performed using amber 03 force field [] […]

PMCID: 4243335
PMID: 25426338
DOI: 10.7717/peerj.679

[…] in the center of a water box with 10 å layer from the structure and with periodic conditions. in order to stabilize the system nacl ions were added. correctness of the model was validated using prosess (). the structure was visualized with pymol (http://www.pymol.org/)., the xre binding site was found using the dbtbs database searching tool (http://dbtbs.hgc.jp/) (). when searching […]

PMCID: 3780550
PMID: 24106696
DOI: 10.1155/2013/172784

[…] threading programs (fugue, hhsearch, muster, ppa, prospect2, sam-t02, sparksx, sp3, ffas, and prc)., all 3d models of baua structure were qualitatively estimated by 4 various independent servers (prosess,vadar, prosa, and qmean). prosess [] server at http://www.prosess.ca (protein structure evaluation suite & server) is a web server designed to evaluate and validate protein structures […]

PMCID: 3348131
PMID: 22590577
DOI: 10.1371/journal.pone.0036612

[…] in the approach presented here. the conformers generated using concoord may be artificially produced but appeared realistic when assessed for geometry and packing by the structure validation server prosess . moreover, the range of cavity characteristics observed was consistent with the variation between crystal structures. although the conformational space of the protein is unlikely to be fully […]


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PROSESS institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada; Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; National Research Council, National Institute for Nanotechnology (NINT), University of Alberta Edmonton, AB, Canada
PROSESS funding source(s)
Supported by Alberta Prion Research Institute; PrioNet; Natural Sciences and Engineering Research Council and Genome Alberta.

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