PredyFlexy statistics

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PredyFlexy specifications

Information


Unique identifier OMICS_09792
Name PredyFlexy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A single FASTA sequence must be provided.
Operating system Unix/Linux
Programming languages Python, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Alexandre G. de Brevern

Information


Unique identifier OMICS_09792
Name PredyFlexy
Interface Web user interface
Restrictions to use None
Input data A single FASTA sequence must be provided.
Programming languages Python, R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Alexandre G. de Brevern

Publication for PredyFlexy

PredyFlexy citations

 (5)
library_books

A general and efficient strategy for generating the stable enzymes

2016
Sci Rep
PMCID: 5036031
PMID: 27667190
DOI: 10.1038/srep33797

[…] To investigate the rigidity of the active center, the PredyFlexy web server was used to predict the normalized B-factor of the best mutant, VarB3. The normalized B-factors of all of the selected flexible residues are listed in . As shown in , the VarB3 m […]

library_books

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158

2016
Sci Rep
PMCID: 4753449
PMID: 26875695
DOI: 10.1038/srep20915

[…] lignment with the domain families defined in the Pfam database when the structure was not available. Flexibility prediction of the sequence encompassing the OBD-OD hinge region was performed with the PredyFlexy server. […]

library_books

Protein flexibility in the light of structural alphabets

2015
Front Mol Biosci
PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] in prediction of flexibility through SA prediction of LSPs, and (iii) in prediction of three classes of flexibility, which are usually limited to two. The method is implemented in a web server named PredyFlexy (http://www.dsimb.inserm.fr/dsimb_tools/predyflexy, de Brevern et al., ), in which the users have access to a confidence index (CI) for assessing the quality of the prediction rate. […]

library_books

An association adjusted consensus deleterious scheme to classify homozygous Mis sense mutations for personal genome interpretation

2013
BioData Min
PMCID: 3892026
PMID: 24365473
DOI: 10.1186/1756-0381-6-24

[…] ssible functional sites of the protein; i.e., sites of protein-protein interactions. Changes in protein dynamics were evaluated by the crystallographic B-factor of Cα atoms. In addition, we also used PredyFlexy [] and FlexPred [,] to predict the dynamic class of an amino acid residue (rigid, intermediate, flexible), and to estimate whether each residue is likely to induce conformational switches w […]

library_books

Virtual screening studies reveal linarin as a potential natural inhibitor targeting CDK4 in retinoblastoma

2013
PMCID: 3826001
PMID: 24250202
DOI: 10.4103/0976-500X.119711

[…] r which MD simulation was initiated to be run for 10ns.[]The stabilized protein was validated using various tools such as Charmm-gui,[] PatchFinderPlus,[] Protein Quality Predictor (ProQ),[] ProSA,[] Predyflexy,[] Psipred,[] and Qsitefinder[] for analyzing electrostatic property, protein flexibility, and binding site analysis. CDK4 is known to have ATP-binding region between 93 and 102 residues. V […]

Citations

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PredyFlexy institution(s)
INSERM, U665, DSIMB; Univ Paris Diderot, Sorbonne Paris Cité, UMR-S665; Institut National de la Transfusion Sanguine (INTS), Paris, France
PredyFlexy funding source(s)
Ministry of Research (France); University of Paris Diderot; Sorbonne Paris Cité; National Institute for Blood Transfusion (INTS, France); Institute for Health and Medical Research (INSERM, France); French Ministry of Research

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