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Advantages of fine-grained side chain conformer libraries
- Source :
- Protein Engineering Design and Selection. 16:963-969
- Publication Year :
- 2003
- Publisher :
- Oxford University Press (OUP), 2003.
-
Abstract
- 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.
- Subjects :
- Physics
Quantitative Biology::Biomolecules
Protein Conformation
Ab initio
Computational Biology
Bioengineering
computer.file_format
Protein Data Bank
Biochemistry
Bond length
Root mean square
Crystallography
Protein structure
Chain (algebraic topology)
Side chain
Amino Acids
Molecular Biology
computer
Conformational isomerism
Biotechnology
Subjects
Details
- ISSN :
- 17410134 and 17410126
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- Protein Engineering Design and Selection
- Accession number :
- edsair.doi.dedup.....4f95b6616279063c96c0e711709aa1e9
- Full Text :
- https://doi.org/10.1093/protein/gzg143