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GSAtools specifications

Information


Unique identifier OMICS_18199
Name GSAtools
Software type Package/Module
Interface Command line interface
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
GROMACS
Maintained Yes

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Maintainer


  • person_outline Alessandro Pandini <>

Publication for GSAtools

GSAtools in publications

 (4)
PMCID: 5690683
PMID: 29108014
DOI: 10.1371/journal.pcbi.1005826

[…] structures (see for a list of the excluded residues). all the residues in the protein were used for the rmsd, rmsf and secondary structure analyses., the analyses were performed using gromacs and gsatools [], together with in-house r scripts using the bio3d [] library. networks were visualised with the xpyder [] plugin for pymol. a more detailed description of the analyses performed […]

PMCID: 4938800
PMID: 27345932
DOI: 10.1016/j.str.2016.05.012

[…] (). the sa provides an enriched string set of local conformational states for accurate reconstruction of protein fold. statistically significant correlations were determined and analyzed with gsatools ()., pfam protein sequence families flimm (pf02154), fligm (pf14821), and fligc (pf01706) () were filtered at 80% redundancy level. psicov-based analysis of residue coevolution between flim […]

PMCID: 5356493
PMID: 26808351
DOI: 10.1021/acs.jctc.5b00992

[…] bio3d r package was used for coordinate manipulation and for the analysis of the archdb database. the encoding of experimental structures and md trajectories with the m32k25 sa was performed with gsatools. structures from the blind loop refinement of the tr464 casp target were independently rescored with rosetta− (ver. 3.3)., the supporting information is available free of charge on the acs […]

PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] their method (camproux et al., ; tung et al., ). an interesting point was the analysis of the correlation between local flexibility and variability in the assignment. thereafter, they have developed gsatools, (http://mathbio.nimr.mrc.ac.uk/wiki/gsatools, pandini et al., ), composed of a set of programs, that encode ensembles of protein conformations into alignments of structural strings using […]


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GSAtools institution(s)
Randall Division of Cell and Molecular Biophysics, King’s College London, London, UK; The Thomas Young Centre for Theory and Simulation of Materials, London, UK; Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK
GSAtools funding source(s)
Supported by the Medical Research Council (U117581331); the British Heart Foundation (FS/12/41/29724); the Biotechnology and Biological Sciences Research Council (BB/I023291/1 and BB/H018409/1).

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