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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
14
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pubmed:dateCreated |
2009-4-2
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pubmed:abstractText |
Here, we computed the aqueous solvation (hydration) free energies of 52 small drug-like molecules using an all-atom force field in explicit water. This differs from previous studies in that (1) this was a blind test (in an event called SAMPL sponsored by OpenEye Software) and (2) the test compounds were considerably more challenging than have been used in the past in typical solvation tests of all-atom models. Overall, we found good correlations with experimental values which were subsequently made available, but the variances are large compared to those in previous tests. We tested several different charge models and found that several standard charge models performed relatively well. We found that hypervalent sulfur and phosphorus compounds are not well handled using current force field parameters and suggest several other possible systematic errors. Overall, blind tests like these appear to provide significant opportunities for improving force fields and solvent models.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-11948581,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-12395429,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-14515375,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-15116359,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-15847482,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-16211538,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-16375397,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-16942107,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-17195160,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-17288412,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-17291029,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-18171044,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-18215013,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-18251538,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19271713-18582013
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Apr
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pubmed:issn |
1520-6106
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pubmed:author |
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pubmed:issnType |
Print
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pubmed:day |
9
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pubmed:volume |
113
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
4533-7
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pubmed:dateRevised |
2010-9-22
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pubmed:meshHeading |
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pubmed:year |
2009
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pubmed:articleTitle |
Predictions of hydration free energies from all-atom molecular dynamics simulations.
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pubmed:affiliation |
Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA. dmobley@gmail.com
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pubmed:publicationType |
Journal Article,
Research Support, N.I.H., Extramural
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