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FlexPred specifications

Information


Unique identifier OMICS_13732
Name FlexPred
Interface Web user interface
Restrictions to use None
Input data It takes a 3D protein structure as input.
Input format PDB
Output data Predicts a fluctuation value for each residue of the protein. An image of the structure with high fluctuation residues, a graph of the predicted fluctuation for each residue number, a link to download file containing the predicted fluctuations.
Output format CSV, PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Daisuke Kihara

Information


Unique identifier OMICS_13732
Name FlexPred
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data It takes a 3D protein structure as input.
Input format PDB
Output data Produces a text file containing the predicted fluctuations for each residue.
Output format TXT
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Daisuke Kihara

Publications for FlexPred

FlexPred citations

 (3)
library_books

Ensemble based evaluation for protein structure models

2016
Bioinformatics
PMCID: 4908346
PMID: 27307633
DOI: 10.1093/bioinformatics/btw262

[…] r the provided flexibility information.We point out that MD simulations are easier to perform than it used to be, for example by using web-based MD tools (; ). Previously, we developed a method named FlexPred, which predicts absolute values of residue fluctuation from a tertiary structure (i.e. a PDB file) of a target protein (), which can be also used to obtain flexibility.At this juncture, it wo […]

library_books

Simple approach for ranking structure determining residues

2016
PeerJ
PMCID: 4924125
PMID: 27366642
DOI: 10.7717/peerj.2136

[…] from the structure-based flexibility as well as the sequence-based intrinsic disorder predisposition of the query proteins. The structural flexibility of these proteins was obtained by utilizing the FlexPred tool that predicts the absolute fluctuations per-residue from a three-dimensional structure using the B–factors of a query protein (, ). The intrinsic disorder propensities per-residue of the […]

library_books

Structure and stability of recombinant bovine odorant binding protein: II. Unfolding of the monomeric forms

2016
PeerJ
PMCID: 4841237
PMID: 27114857
DOI: 10.7717/peerj.1574

[…] hat the monomeric GCC-bOBP has the overall fold almost identical to that of the pOBP. Next, we analyzed how introduced mutations affected the structural flexibility of bOBP utilizing the power of the FlexPred tool that rapidly predicts absolute per-residue fluctuations from a three-dimensional structure of a query protein (). Results of this analysis are shown in which clearly indicates that the […]


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FlexPred institution(s)
Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN, USA; Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warszawa, Poland; Department of Biological Sciences, College of Science, Purdue University, West Lafayette, IN, USA; Department of Computer Science, College of Science, Purdue University, University Street, West Lafayette, IN, USA
FlexPred funding source(s)
This work was partly supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM097528) and the National Science Foundation (IIS1319551, DBI1262189, IOS1127027).

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