Smooth Backbone-Dependent Rotamer Library 2010
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions
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.
License
As of July 25, 2019, it is based on a Creative Commons CC BY 4.0 license. The license for the 2010 backbone-dependent rotamer library is now less restrictive than it was previously. It is the same for both academia and industry: The library is free, redistributable, and modifiable as long as you acknowledge the source of the library. See details in the link.
License
Documentation
Smooth surfaces for protein side chains
A component of a new backbone-dependent rotamer library is shown on the left. The probability of the trans rotamer of valine is plotted as a function of the backbone dihedrals φ and ψ. The residues in the alpha-helix, parallel beta-sheet and left-handed helix regions are depicted as a snowboarder, a skier and a luger respectively. Their heads are the side-chain Cβ atoms. The arms have the same trans-rotamer side-chain conformation while their legs have different backbone conformations in accordance with the residue locations on the Ramachandran map. The heights of the hills are proportional to the backbone-dependent probability of the <trans> rotamer, relative to the <g+> and <g-> rotamers.
Article
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Shapovalov, M.V., and Dunbrack, R.L., Jr., Structure 2011, 19, 844-858. Article