Rotamer Library specifications

Information


Unique identifier OMICS_25916
Name Rotamer Library
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
catdcd, numpy, matplotlib, MDAnalysis
Maintained Yes

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Maintainers


  • person_outline Ben Corry <>
  • person_outline Katarzyna Walczewska-Szewc <>

Publication for Rotamer Library

Rotamer Library in publications

 (255)
PMCID: 5923235
PMID: 29703992
DOI: 10.1038/s41467-018-03727-6

[…] presence of agonist. the combinatorial models with the lowest rss and aics were then selected for further analysis., theoretical deer distance distributions were generated using mmm (with the mtsl rotamer library at 175 k) for the nts1 dimer models with dimer interfaces tm1–2–h8 based on ß1ar, tm3–4 based on h1r, and tm5–6 based on µor for ten snapshots of the md simulations for each model, […]

PMCID: 5920107
PMID: 29700324
DOI: 10.1038/s41598-018-24688-2

[…] (insert fig. )., a molecular model of sti w111c monomer was developed replacing trp111 by cys with modeller software using as template the rmn model n°1 of sti soluble structure. a disulfide-bridge rotamer library with 83 members was build from the pdbepisa web server (table s in the supporting material). the variation of dihedral angles (χ3) around the cβ-s-s-cβ atoms for each disulfide-bridge […]

PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] complexes which uses a novel dars (decoys as reference state) reference set. the last term, erp, is a statistical energy term associated with a set of rotamers selected from the backbone-dependent rotamer library. the weight set of the energy function is adopted according to the selections in gray et al.., we validated our algorithm on a comprehensive benchmark of 230 protein complexes […]

PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] a review of the foldx accuracy., to construct pr1 mutant structures, we used the buildmodel command of foldx suite. this command introduces a mutation on the wild-type structure using a side-chain rotamer library. it then optimizes the configurations of the side chains of amino acids in the vicinity of the mutated residue. in foldx, the mutated residue vicinity was defined as residues […]

PMCID: 5865177
PMID: 29572541
DOI: 10.1038/s41598-018-22912-7

[…] a disulfide bridge was built between cys208 and cys209; ile291, thr439 and tyr110 were mutated back to their native side chain, ala, ser and ala, respectively, using ucsf-chimera and the dunbrack rotamer library. chloride and sodium (placed at the na1 and na2 sites) ions and the ligand (serotonin or paroxetine) were not included in the coarse grain model because its resolution (see below) […]


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Rotamer Library institution(s)
Research School of Biology, Australian National University, Acton, ACT Australia; Institute of Experimental Physics, University of Gdansk, Poland
Rotamer Library funding source(s)
Partially supported by the Foundation for Polish Science with the International PhD Project MPD/2009-3/4.

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