PredyFlexy protocols

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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

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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 in pipelines

 (3)
2016
PMCID: 4753449
PMID: 26875695
DOI: 10.1038/srep20915

[…] 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., structure comparisons and superpositions were performed using the molecular graphics program coot. figures were prepared using pymol (the pymol molecular graphics system, version […]

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

[…] solutions were maintained at a starting temperature for 15 min. the melting temperature, tm, obtained from the dsc experiments corresponded to the maximum of the transition peak., the web server predyflexy (http://www.dsimb.inserm.fr/dsimb_tools/predyflexy) was used to predict the normalized b-factor based on a library composed of structural prototypes and molecular dynamic simulations. […]

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

[…] 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 […]


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PredyFlexy in publications

 (5)
PMCID: 5036031
PMID: 27667190
DOI: 10.1038/srep33797

[…] phenylalanine by neutral or aromatic residues did not change the conformation of the binding pocket and thus retained the substrate preference., 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 […]

PMCID: 4753449
PMID: 26875695
DOI: 10.1038/srep20915

[…] obd and od in all viral helicases discussed herein (). moreover, a number of residues within these unstructured regions are predicted to be highly flexible with a good confidence index using the predyflexy server. the presence of a hinge is supported by the available experimental structures of viral reps containing the od, which consistently show the presence of an unstructured amino acid […]

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., […]

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

[…] 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 […]

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

[…] 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. […]


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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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