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ResProx specifications

Information


Unique identifier OMICS_17108
Name ResProx
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline David Wishart

Additional information


http://www.resprox.ca/how_to_use.html

Publication for ResProx

ResProx citations

 (10)
library_books

Insights from the protein protein interaction network analysis of Mycobacterium tuberculosis toxin antitoxin systems

2017
Bioinformation
PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] A (). The 3D models generated in the study were of reliable quality as assessed by various structural assessment reports such as PROCHECK of swiss model server, ERRAT, ProSA-web, ProQ, MOLPROBITY and ResProx. In addition, active site of VapC9 and VapC10 was identified by Metapocket v2.0. The generated homology models and active site determined by metapocket v2.0 of VapC9 and VapC10, respectively a […]

library_books

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach

2017
Front Plant Sci
PMCID: 5447077
PMID: 28611792
DOI: 10.3389/fpls.2017.00819

[…] model methods including PROCHECK (Laskowski et al., ), Qualitative Model Energy Analysis (QMEAN; Benkert et al., ), Protein Structural Analysis (ProSA; Wiederstein and Sippl, ), Resolution by Proxy (ResProx; Berjanskii et al., ). Based on PROCHECK analysis of PDBSum results it was found that total 100.0% of the residues occurred in the most favored regions (A, B, L), 0.0% residues were found in a […]

library_books

Molecular docking studies of 3 bromopyruvate and its derivatives to metabolic regulatory enzymes: Implication in designing of novel anticancer therapeutic strategies

2017
PLoS One
PMCID: 5413015
PMID: 28463978
DOI: 10.1371/journal.pone.0176403

[…] which is a reliable statistical potential to assess quality of homology models in protein structure prediction []. The generated SDH model was further validated with RAMPAGE, PDBSum, SAVES, VADAR and ResProx servers. RAMPAGE analysis of the predicted SDH model showed 97.7% residues in favored region, which is close to the requisite percentage of 98 for validating a model (). Favoured regions of Ra […]

library_books

The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer

2016
Front Mol Biosci
PMCID: 5156680
PMID: 28018905
DOI: 10.3389/fmolb.2016.00078

[…] he 501 frames extracted from each MD ensemble. Differences between average and experimentally obtained distances were then calculated.For each MD ensemble we also predicted the resolution value using Resprox (Berjanskii et al., ) and compared it to the predicted resolution of the NMR ensemble deposited in the PDB (PDB entry 2FI2). […]

library_books

Identification of Plasmodium falciparum Translation Initiation eIF2β Subunit: Direct Interaction with Protein Phosphatase Type 1

2016
Front Microbiol
PMCID: 4881399
PMID: 27303372
DOI: 10.3389/fmicb.2016.00777

[…] The Robetta server (http://robetta.bakerlab.org/) was used for tertiary modeling. The best structure was ranked using the RESPROX (Berjanskii et al., ) qualifying server. Finally, the structure was prepared using the Schrodinger's Maestro (Schrödinger: Schrödinger maestro Package In: maestro, version 99. New York: LLC; 2 […]

library_books

Fast evolutionary rates associated with functional loss in class I glucose transporters of Schistosoma mansoni

2015
BMC Genomics
PMCID: 4653847
PMID: 26584526
DOI: 10.1186/s12864-015-2144-6

[…] structure prediction servers, namely FOLDpro [], I-TASSER [], 3D-Jigsaw [], LOOPP [], Phyre2 [] and SwissModel []. To assess the quality of the output models and to choose the top candidates we used Resprox [], Qmean [], ModFOLD []. We then manually inspected the top three models of each SGTP to determine any unresolved secondary structures (i.e., α-helices).The top candidate model structures wer […]

Citations

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ResProx institution(s)
Department of Computing Science, University of Alberta, Edmonton, AB, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada
ResProx funding source(s)
Supported by the Alberta Prion Research Institute (APRI), PrioNet, and the Natural Sciences and Engineering Research Council (NSERC).

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