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Rotamer Libraries citations(40)
Computer aided design of amino acid based therapeutics: a review
[…] 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 […]
Efficient conformational ensemble generation of protein bound peptides
[…] 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 […]
An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences
[…] 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 […]
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.
[…] 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 […]
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts
[…] 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 […]
Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model
[…] 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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