Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes
dc.contributor.author | Chang, Max W. | en_US |
dc.contributor.author | Belew, Richard K. | en_US |
dc.contributor.author | Carroll, Kate S. | en_US |
dc.contributor.author | Olson, Arthur J. | en_US |
dc.contributor.author | Goodsell, David S. | en_US |
dc.date.accessioned | 2008-07-01T14:08:05Z | |
dc.date.available | 2009-08-12T18:32:18Z | en_US |
dc.date.issued | 2008-08 | en_US |
dc.identifier.citation | Chang, Max W.; Belew, Richard K.; Carroll, Kate S.; Olson, Arthur J.; Goodsell, David S. (2008). "Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes." Journal of Computational Chemistry 29(11): 1753-1761. <http://hdl.handle.net/2027.42/60220> | en_US |
dc.identifier.issn | 0192-8651 | en_US |
dc.identifier.issn | 1096-987X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/60220 | |
dc.identifier.uri | http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=18351616&dopt=citation | en_US |
dc.description.abstract | The results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand–protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a method that estimates the extent of the local energetic well by looking at the scatter of conformations within clustered results, and an RMSD-based method that uses the overall scatter and clustering of all conformations. We have also directly characterized the local energy landscape by randomly sampling around docked conformations. The simple cluster size method shows the best performance, improving the identification of correct conformations in multiple docking experiments. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 | en_US |
dc.format.extent | 352043 bytes | |
dc.format.extent | 3118 bytes | |
dc.format.mimetype | application/pdf | |
dc.format.mimetype | text/plain | |
dc.publisher | Wiley Subscription Services, Inc., A Wiley Company | en_US |
dc.subject.other | Chemistry | en_US |
dc.subject.other | Theoretical, Physical and Computational Chemistry | en_US |
dc.title | Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Chemical Engineering | en_US |
dc.subject.hlbsecondlevel | Chemistry | en_US |
dc.subject.hlbsecondlevel | Materials Science and Engineering | en_US |
dc.subject.hlbtoplevel | Engineering | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.contributor.affiliationum | Department of Chemistry and the Life Sciences Institute, University of Michigan at Ann Arbor, Ann Arbor, Michigan 48109 | en_US |
dc.contributor.affiliationother | Bioinformatics Program, University of California at San Diego, La Jolla, California 92093 | en_US |
dc.contributor.affiliationother | Bioinformatics Program, University of California at San Diego, La Jolla, California 92093 ; Department of Cognitive Science, University of California at San Diego, La Jolla, California 92093 | en_US |
dc.contributor.affiliationother | Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 | en_US |
dc.contributor.affiliationother | Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 ; Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 | en_US |
dc.identifier.pmid | 18351616 | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/60220/1/20936_ftp.pdf | |
dc.identifier.doi | http://dx.doi.org/10.1002/jcc.20936 | en_US |
dc.identifier.source | Journal of Computational Chemistry | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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