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Rotamer Libraries specifications

Information


Unique identifier OMICS_15559
Name Rotamer Libraries
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Documentation


Publication for Rotamer Libraries

Rotamer Libraries citations

 (40)
library_books

Computer aided design of amino acid based therapeutics: a review

2018
Drug Des Devel Ther
PMCID: 5958949
DOI: 10.2147/DDDT.S159767

[…] chain of each amino acid. For example, the simplest amino acids including alanine and glycine have only one rotamer status, while the bigger amino acids have >80 diverse rotamer statuses.A variety of rotamer libraries including backbone- dependent, secondary structure-dependent and backbone-independent libraries have been developed for protein design., By using a rotamer library, one can discretiz […]

library_books

Efficient conformational ensemble generation of protein bound peptides

2017
J Cheminform
PMCID: 5700017
PMID: 29168051
DOI: 10.1186/s13321-017-0246-7

[…] We have constructed two backbone-dependent rotamer libraries for peptide model building. The first library is called single-letter library, in which each rotamer consists of one amino acid residue (see Fig. a for an example). Therefore, we hav […]

library_books

An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

2017
Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] ead-end elimination, Monte Carlo sampling and simulated annealing are usually used to sample the most probable rotamer (side-chain conformation), based on the local conformation of the backbone, from rotamer libraries such as that used by SCWRL (Krivov et al., 2009). Once the model has been produced, it is usually refined to minimize un­favourable collisions between atoms. This is usually performe […]

library_books

Model free extraction of spin label position distributions from pseudocontact shift data† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc03736d Click here for additional data file.

2017
PMCID: 5426344
PMID: 28553510
DOI: 10.1039/c6sc03736d

[…] or protons. presents the comparison between the distance distributions between lanthanide ions in tags at different sites obtained using three physically different methods: DEER, PCS (this work) and rotamer libraries., For three out of four tagging site pairs, the agreement of the PCS data with the DEER data is very good and significantly better than the agreement of the rotamer library predictio […]

library_books

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

2016
Biochemistry
PMCID: 5007558
PMID: 27490953
DOI: 10.1021/acs.biochem.6b00444

[…] the backbone must be fixed, as the NCB will have flexibilities different from those of a linear chain of three singly bonded atoms. The final key point in the addition of NCBs is the creation of new rotamer libraries for the side chain. Even if the side-chain atoms are identical to those of a canonical side chain, the chemical change in the backbone will cause different flexibilities, due to ster […]

library_books

Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

2016
PLoS One
PMCID: 4887040
PMID: 27243223
DOI: 10.1371/journal.pone.0156559

[…] r-library-free approach. Here, the catalytic residues can adopt unusual high-energy structures that may be required by the enzyme reaction, but such geometries are not always included in conventional rotamer libraries because the rotamers in these libraries are always low-energy conformers of the naturally occurring amino acids. In the initial version of ProdaMatch [], the loop-closure problems we […]

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