CABS-flex statistics

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CABS-flex specifications

Information


Unique identifier OMICS_04015
Name CABS-flex
Interface Web user interface
Restrictions to use None
Input data Protein structure
Input format PDB
Output data An ensemble of protein models reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others).
Output format PDB
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Sebastian Kmiecik <>

Information


Unique identifier OMICS_04015
Name CABS-flex
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 0.9.12
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sebastian Kmiecik <>

Publications for CABS-flex

CABS-flex in publications

 (5)
PMCID: 5785596
PMID: 29080206
DOI: 10.1007/s13361-017-1830-9

[…] average prediction. peptide coverage was drawn using draw map []. sequence alignment was performed in align, uniprot clustal omega []. the gw182 flexibility and normal modes were checked by cabs-flex [] and [email protected] [] servers., far-uv cd spectra were recorded with the mos-450/af-cd spectrometer from bio-logic, with a xe lamp as a source of light, in the wavelength range of 190–260 nm, […]

PMCID: 5598929
PMID: 28910295
DOI: 10.1371/journal.pone.0183564

[…] the position of the loops in our original energy minimized models. to further investigate the potential relevance of the loop structures lining the substrate binding pocket in these enzymes, we used cabs-flex to simulate protein structure fluctuations and assess the range of motion for these loops []. the dynamic models revealed that the range of movement in the loop structure comprised […]

PMCID: 5511257
PMID: 28710462
DOI: 10.1038/s41598-017-05657-7

[…] structure of the inhibitor/enzyme complex, cys15-cys51 disulfide is covered by the inhibitor c-tail only because it is docked and fixed in the active site of the carboxypeptidase moiety. we used the cabs-flex algorithm to simulate the structural flexibility of non-bound nvci and the generated structural models strongly suggest that the c-tail would be flexible in solution and not expected […]

PMCID: 5479843
PMID: 28638118
DOI: 10.1038/s41598-017-03323-6

[…] the molecular dynamics simulations the best model generated by i-tasser was used., residues with highest degree of flexibility were predicted using a coarse-grained dynamics approach implemented in cabs-flex server. here, high root mean square fluctuation (rmsf) value is indicative of high residue flexibility. for several other proteins, results of such simulations have already been proved […]

PMCID: 4423475
PMID: 25951439
DOI: 10.1038/srep09705

[…] of the c-terminal tail of the protein () and predicted that a conformational shift to a larger binding site (volume = 233.37 å3) occurred in the protein (). the results of a study performed with the cabs-flex server (http://biocomp.chem.uw.edu.pl/cabsflex/index.php), which implements one of the best algorithms specialized in residue fluctuation analysis, were also in agreement […]


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CABS-flex institution(s)
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Warsaw, Poland; Faculty of Physics, University of Warsaw, Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
CABS-flex funding source(s)
Supported by the National Science Center (NCN, Poland) Grant [MAESTRO2014/14/A/ST6/00088].

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