The Supplementary material referred to in this article can be found at http://www.interscience.wiley.com/jpages/0887-3585/suppmat/index.html/.
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Research Article
The penultimate rotamer library†
Article first published online: 12 JUN 2000
DOI: 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2
Copyright © 2000 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Volume 40, Issue 3, pages 389–408, 15 August 2000
Additional Information
How to Cite
Lovell, S. C., Word, J. M., Richardson, J. S. and Richardson, D. C. (2000), The penultimate rotamer library. Proteins, 40: 389–408. doi: 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2
- †
Publication History
- Issue published online: 12 JUN 2000
- Article first published online: 12 JUN 2000
- Manuscript Accepted: 14 MAR 2000
- Manuscript Received: 20 DEC 1999
Funded by
- National Institutes of Health. Grant Number: GM-15000
Keywords:
- side-chain rotamer library;
- all-atom contact analysis;
- structure validation;
- reversed leucines;
- explicit hydrogens;
- van der Waals analysis
Abstract
All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors ≥40 or van der Waals overlaps ≥0.4 Å) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of χ angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389–408. © 2000 Wiley-Liss, Inc.