Cited by 1,000Protein Structure and DynamicsEnzyme Structure and FunctionRNA and protein synthesis mechanisms

A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions

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Shapovalov, Maxim V., Dunbrack, Roland L.·2011·Structure

Abstract

Rotamer libraries are used in protein structure determination, prediction, and design. The backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles, and variances as a function of the backbone dihedral angles. Structure prediction and design methods that employ backbone flexibility would strongly benefit from smoothly varying probabilities and angles. A new version of the backbone-dependent rotamer library has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances. This formulation allows for evaluation of the rotamer probabilities, mean angles, and variances as a smooth and continuous function of phi and psi. Continuous probability density estimates for the nonrotameric degrees of freedom of amides, carboxylates, and aromatic side chains have been modeled as a function of the backbone dihedrals and rotamers of the remaining degrees of freedom. New backbone-dependent rotamer libraries at varying levels of smoothing are available from http://dunbrack.fccc.edu.

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Crossref · 10.1016/j.str.2011.03.019

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  • The joint distribution of side-chain torsion angles of a residue r, conditional on its backbone dihedral angles, is approximated by a protein-dependent side-chain rotamer library.

    “p(⋅|ϕr, ψr, r) stands for the joint distribution of side-chain torsion angles of the residue r, which is approximated by a protein-dependent side-chain rotamer library [64].”

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Authors
Shapovalov, M. V., & Dunbrack, R. L.
Affiliations
Fox Chase Cancer Center (US)
Corresponding author
Dunbrack, Roland L.
Venue
Structure
Publisher
Elsevier BV
Published
2011-06
Volume
19
Issue
6
Pages
844-858
ISSN
0969-2126 (ISSN-L)
OpenAlex
W2011658408
Cited by
1,000
References
52
Citations by year
2026: 72 · 2025: 113 · 2024: 124 · 2023: 108 · 2022: 123 · 2021: 97 · 2020: 72 · 2019: 44 · 2018: 48 · 2017: 35 · 2016: 37 · 2015: 45 · 2014: 32 · 2013: 28 · 2012: 18
FWCI
10.66
Type
journal article
Language
en
Open access
Locations
  • Structure (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institute of General Medical Sciences (R01-GM84453, P20 GM76222, P20GM076222, R01GM084453)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
dihedral angle, adaptive kernel density estimation, protein structure prediction, protein design, aromatic side chains
MeSH terms
Algorithms, Amino Acids, Computer Simulation, Models, Molecular, Protein Conformation, Proteins, Thermodynamics, Computational Biology

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