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FRST specifications

Information


Unique identifier OMICS_18586
Name FRST
Alternative name Function of RAPDF Solvation and Torsion potentials
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Version 1.2
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Additional information


Access to the desktop version available upon request.

Information


Unique identifier OMICS_18586
Name FRST
Alternative name Function of RAPDF Solvation and Torsion potentials
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.2
Stability Stable
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Additional information


Access to the desktop version available upon request.

Publication for Function of RAPDF Solvation and Torsion potentials

FRST citations

 (17)
library_books

Extent of Night Warming and Spatially Heterogeneous Cloudiness Differentiate Temporal Trend of Greenness in Mountainous Tropics in the New Century

2017
Sci Rep
PMCID: 5264156
PMID: 28120949
DOI: 10.1038/srep41256

[…] tasets, which include the global forest cover change in 2000–2012 at 30 m resolution and the global forest area at country level provided by the World Bank (http://data.worldbank.org/indicator/AG.LND.FRST.ZS).In order to investigate the climate impact on greenness, we intended to identify those areas without LCLUC based on land cover maps. Unfortunately accurate high resolution land cover maps are […]

library_books

The C terminal domain of TPX2 is made of alpha helical tandem repeats

2016
BMC Struct Biol
PMCID: 5080731
PMID: 27782824
DOI: 10.1186/s12900-016-0070-8

[…] accession number: AAF81694) was uploaded in FASTA format to I-TASSER and tertiary structures were predicted in PDB format for individual repeats. Energetic stability of each repeat was evaluated with FRST Energy Validation software [] and each repeat model was examined for its compatibility with the sequence alignment. An initial structural model of X. laevis TPX2 was assembled with PyMol (version […]

library_books

Sorting protein decoys by machine learning to rank

2016
Sci Rep
PMCID: 4987638
PMID: 27530967
DOI: 10.1038/srep31571

[…] unction RW, and contains a side-chain orientation-dependent energy term.The evaluation scores from other model quality assessment programs are also extracted as additional features, which include the Frst, ProQ, RFMQA, SIFT and SELECTpro software.The Frst software’s output is based on four knowledge-based potentials: RAPDF potential, SOLV potential, HYDB potential, and TORS potential, and the Frst […]

library_books

The RING 2.0 web server for high quality residue interaction networks

2016
Nucleic Acids Res
PMCID: 4987896
PMID: 27198219
DOI: 10.1093/nar/gkw315

[…] nclude secondary structure, vertex degree (the number of directly connected nodes), experimental uncertainty for X-ray structures (i.e. Cα B-factor), conformational energy preferences determined with FRST () and TAP (), conservation (Shannon entropy) and cumulative mutual information (MI) (), calculated from PSI-BLAST profiles (). Interaction energies have been derived from the literature, in part […]

library_books

Computational analysis of prolyl hydroxylase domain containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans

2016
Sci Rep
PMCID: 4709589
PMID: 26754054
DOI: 10.1038/srep18716

[…] re was predicted ab initio with Rosetta using an optimized protocol for intrinsically disordered proteins. The quality of proposed PHD2 mutant models, as well as LIMD1 structures, were evaluated with FRST and QMEANclust, while molecular structures were visualized with Chimera. Mutations affecting charged residues were investigated with BLUUES. Networks of interacting residues of wild type and muta […]

library_books

2mit, an Intronic Gene of Drosophila melanogaster timeless2, Is Involved in Behavioral Plasticity

2013
PLoS One
PMCID: 3786989
PMID: 24098788
DOI: 10.1371/journal.pone.0076351

[…] e to generate a raw model, which is then completed by modeling the divergent regions with a fast divide and conquer method []. Side chains were placed with SCWRL3 [] and the energy was evaluated with FRST []. The final models were subjected to a short steepest descent energy minimization with GROMACS [] to remove energy hotspots before calculating the electrostatic surface with APBS []. The struct […]

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FRST institution(s)
Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
FRST funding source(s)
Supported by a “Rientro dei cervelli” grant from the Italian Ministry for Education, University and Research (MIUR) and by Telethon (Italy), grant number B057-I.

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