| Literature DB >> 26745530 |
Clare-Louise Towse1, Steven J Rysavy2, Ivan M Vulovic3, Valerie Daggett4.
Abstract
Most rotamer libraries are generated from subsets of the PDB and do not fully represent the conformational scope of protein side chains. Previous attempts to rectify this sparse coverage of conformational space have involved application of weighting and smoothing functions. We resolve these limitations by using physics-based molecular dynamics simulations to determine more accurate frequencies of rotameric states. This work forms part of our Dynameomics initiative and uses a set of 807 proteins selected to represent 97% of known autonomous protein folds, thereby eliminating the bias toward common topologies found within the PDB. Our Dynameomics derived rotamer libraries encompass 4.8 × 10(9) rotamers, sampled from at least 51,000 occurrences of each of 93,642 residues. Here, we provide a backbone-dependent rotamer library, based on secondary structure ϕ/ψ regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication.Entities:
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Year: 2016 PMID： 26745530 PMCID： PMC4715459 DOI： 10.1016/j.str.2015.10.017
Source DB: PubMed Journal: Structure ISSN： 0969-2126 Impact factor: 5.006