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Citations per year

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

This map represents all the scientific publications referring to PROSESS per scientific context
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Protocols

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 citations

 (7)
library_books

Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism

2017
Sci Rep
PMCID: 5596018
PMID: 28900197
DOI: 10.1038/s41598-017-11736-6

[…] s 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 sim […]

library_books

Structural Models of Zebrafish (Danio rerio) NOD1 and NOD2 NACHT Domains Suggest Differential ATP Binding Orientations: Insights from Computational Modeling, Docking and Molecular Dynamics Simulations

2015
PLoS One
PMCID: 4374677
PMID: 25811192
DOI: 10.1371/journal.pone.0121415

[…] rver indicated no bad bond lengths and angles for the predicted models. The H-bond energy, packing defect, bump score, radius of gyration (Rg) and deviation of Θ angles calculated at VADAR, GeNMR and PROSESS servers were within the cut-off range, as summarized in . […]

call_split

Protein expression, characterization and activity comparisons of wild type and mutant DUSP5 proteins

2014
BMC Biochem
PMCID: 4299175
PMID: 25519881
DOI: 10.1186/s12858-014-0027-0
call_split See protocol

[…] onfidence 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. […]

call_split

Bacillus anthracis pXO1 plasmid encodes a putative membrane bound bacteriocin

2014
PeerJ
PMCID: 4243335
PMID: 25426338
DOI: 10.7717/peerj.679
call_split See protocol

[…] laced 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 a sequence […]

library_books

In Silico Determination and Validation of Baumannii Acinetobactin Utilization A Structure and Ligand Binding Site

2013
Biomed Res Int
PMCID: 3780550
PMID: 24106696
DOI: 10.1155/2013/172784

[…] 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 solved b […]

library_books

Immunoinformatic Docking Approach for the Analysis of KIR3DL1/HLA B Interaction

2013
Biomed Res Int
PMCID: 3747338
PMID: 23984333
DOI: 10.1155/2013/283805

[…] [] and allele frequency in different human populations [] (). Quality of the models based on X-ray crystallography experiments or homology modeling in SWISS model workspace [] has been evaluated with PROSESS server []. In order to compare different HLA-B alleles, peptides with the similar EC50 (200 nM) were selected as references from IEDB database []. In the analysis of HLA-B alleles belonging to […]


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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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