ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures
dc.contributor.author | Park, Jungkap | |
dc.contributor.author | Saitou, Kazuhiro | |
dc.date.accessioned | 2014-12-09T19:02:17Z | |
dc.date.available | 2014-12-09T19:02:17Z | |
dc.date.issued | 2014-09-18 | |
dc.identifier.citation | BMC Bioinformatics. 2014 Sep 18;15(1):307 | |
dc.identifier.uri | https://hdl.handle.net/2027.42/109687 | en_US |
dc.description.abstract | Abstract Background Multibody potentials accounting for cooperative effects of molecular interactions have shown better accuracy than typical pairwise potentials. The main challenge in the development of such potentials is to find relevant structural features that characterize the tightly folded proteins. Also, the side-chains of residues adopt several specific, staggered conformations, known as rotamers within protein structures. Different molecular conformations result in different dipole moments and induce charge reorientations. However, until now modeling of the rotameric state of residues had not been incorporated into the development of multibody potentials for modeling non-bonded interactions in protein structures. Results In this study, we develop a new multibody statistical potential which can account for the influence of rotameric states on the specificity of atomic interactions. In this potential, named “rotamer-dependent atomic statistical potential” (ROTAS), the interaction between two atoms is specified by not only the distance and relative orientation but also by two state parameters concerning the rotameric state of the residues to which the interacting atoms belong. It was clearly found that the rotameric state is correlated to the specificity of atomic interactions. Such rotamer-dependencies are not limited to specific type or certain range of interactions. The performance of ROTAS was tested using 13 sets of decoys and was compared to those of existing atomic-level statistical potentials which incorporate orientation-dependent energy terms. The results show that ROTAS performs better than other competing potentials not only in native structure recognition, but also in best model selection and correlation coefficients between energy and model quality. Conclusions A new multibody statistical potential, ROTAS accounting for the influence of rotameric states on the specificity of atomic interactions was developed and tested on decoy sets. The results show that ROTAS has improved ability to recognize native structure from decoy models compared to other potentials. The effectiveness of ROTAS may provide insightful information for the development of many applications which require accurate side-chain modeling such as protein design, mutation analysis, and docking simulation. | |
dc.title | ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures | |
dc.type | Article | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/109687/1/12859_2014_Article_6637.pdf | |
dc.identifier.doi | 10.1186/1471-2105-15-307 | en_US |
dc.language.rfc3066 | en | |
dc.rights.holder | Park and Saitou; licensee BioMed Central Ltd. | |
dc.date.updated | 2014-12-09T19:02:18Z | |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.