Side-chain rotamer library specifications

Information


Unique identifier OMICS_26609
Name Side-chain rotamer library
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Barry Honig <>

Publication for Side-chain rotamer library

Side-chain rotamer library in publications

 (13)
PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] (2018) for 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 […]

PMCID: 4559433
PMID: 26335248
DOI: 10.1371/journal.pone.0130433

[…] protein structure and then reconstructed de novo, given a fixed backbone environment for the rest of the protein. all segment side chains and those within 10√• of the segment are modeled based on a side chain rotamer library [] that does not include the native side chain conformations., the long loops benchmark [] analogously tests whether protocols are able to reconstruct loop segments […]

PMCID: 4533164
PMID: 26238798
DOI: 10.1038/srep12501

[…] refinement. in structural quality assessment, if the normalized residue score is above 2.0, the side chains involved will be subjected to an in-house side-chain modeling program that combines an xyz side-chain rotamer library, dfire, and a faster search algorithm, to obtain the optimal conformation. a 50-step energy minimization using tinker and opls all-atom force field is performed to relax […]

PMCID: 4439022
PMID: 25993617
DOI: 10.1371/journal.pone.0128360

[…] [, ]. mutations such as point mutations were handled by scap in our study. in this modeling, the amber force field was selected in accordance with following amber simulations, and the large side-chain rotamer library was used for a thorough structural search. similarly, loopy predicts loops and mutated sequences for protein chains. multiple initial conformations of the predicted/mutated […]

PMCID: 4084637
PMID: 24992528
DOI: 10.1371/journal.pone.0099881

[…] visual inspection and further side-chain modeling., in step 4, problematic residues are optimized using a side-chain modeling/prediction program that combines a statistical potential (dfire), an xyz side-chain rotamer library and a combinatorial search algorithm named faster ., we used tm-align , a structural alignment algorithm, as core engine for scaffolding search. compared with other widely […]


To access a full list of publications, you will need to upgrade to our premium service.

Side-chain rotamer library institution(s)
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Side-chain rotamer library funding source(s)
Supported by NIH grant GM-30518.

Side-chain rotamer library reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Side-chain rotamer library