ArticleStructure (London, England : 1993)2011
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.
Article in Structure (London, England : 1993), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 524 papers.
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524 citing papers in PubMed.
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- NuConf: a rotamer library for DNA and RNA and its implementation in the protein design software MUMBO.Scientific reports · 2026Article
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464 more citing papers are in PubMed but not listed here.
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2 authors.
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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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