title: New Dynamic Rotamer Libraries: Data-Driven Analysis of Side-Chain Conformational Propensities.
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.
authors.affiliation: Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA.
authors.forename: Clare-Louise
authors.initials: CL
authors.lastname: Towse
authors.affiliation: Biomedical and Health Informatics Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Rysavy
authors.affiliation: Molecular Engineering Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA.
authors.forename: Ivan M
authors.initials: IM
authors.lastname: Vulovic
authors.affiliation: Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA; Biomedical and Health Informatics Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA; Molecular Engineering Program, University of Washington, Box 355013, Seattle, WA 98195-5013, USA. Electronic address: daggett@uw.edu.
authors.forename: Valerie
authors.initials: V
authors.lastname: Daggett
mesh_terms: D000818:Animals; D006801:Humans; D007536:Isomerism; D056004:Molecular Dynamics Simulation; D019151:Peptide Library; D011487:Protein Conformation; D012984:Software; D014452:Ubiquitins / Q000737:chemistry
chemical_list: D019151:Peptide Library; D014452:Ubiquitins