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Protein Engineering vol. 16 no. 12 pp. 963-969, 2003
© 2003 Oxford University Press

Advantages of fine-grained side chain conformer libraries

Reshma P. Shetty1, Paul I.W. de Bakker2,3, Mark A. DePristo and Tom L. Blundell

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK 1Present address: Biological Engineering Division, Massachusetts Institute of Technology, Boston, MA 02139, USA 2Present address: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA

3 To whom correspondence should be addressed. e-mail: debakker{at}molbio.mgh.harvard.edu

We compare the modelling accuracy of two common rotamer libraries, the Dunbrack–Cohen and the ‘Penultimate’ rotamer libraries, with that of a novel library of discrete side chain conformations extracted from the Protein Data Bank. These side chain conformer libraries are extracted automatically from high-quality protein structures using stringent filters and maintain crystallographic bond lengths and angles. This contrasts with traditional rotamer libraries defined in terms of {chi} angles under the assumption of idealized covalent geometry. We demonstrate that side chain modelling onto native and near-native main chain conformations is significantly more successful with the conformer libraries than with the rotamer libraries when solely considering excluded-volume interactions. The rotamer libraries are inadequate to model side chains without atomic clashes on over 20% of targets if the backbone is held fixed in the native conformation. An algorithm is described for simultaneously modelling both main chain and side chain atoms during discrete ab initio sampling. The resulting models have equivalent root mean square deviations from the experimentally determined protein loops as models from backbone-only ensembles, indicating that all-atom modelling does not detract from the accuracy of conformational sampling.

Received April 30, 2003; revised October 24, 2003; accepted October 30, 2003


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