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231224s2012 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.22984
|2 doi
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|a pubmed25n0724.xml
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|a (NLM)22522665
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|a DE-627
|b ger
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|e rakwb
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|a eng
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|a Sindhikara, Daniel J
|e verfasserin
|4 aut
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|a Placevent
|b an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase
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|c 2012
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Completed 28.09.2012
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|a Date Revised 16.11.2017
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a Copyright © 2012 Wiley Periodicals, Inc.
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|a We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three-dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D-RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI-272 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39-0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is extremely useful for examining multiple specific solvent-solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a Oligopeptides
|2 NLM
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|a Solvents
|2 NLM
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|a HIV Protease
|2 NLM
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|a EC 3.4.23.-
|2 NLM
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|a Proton-Translocating ATPases
|2 NLM
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|a EC 3.6.3.14
|2 NLM
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|a kynostatin 272
|2 NLM
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|a MUL0OE3YBF
|2 NLM
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|a Yoshida, Norio
|e verfasserin
|4 aut
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|a Hirata, Fumio
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 33(2012), 18 vom: 05. Juli, Seite 1536-43
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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|g volume:33
|g year:2012
|g number:18
|g day:05
|g month:07
|g pages:1536-43
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|u http://dx.doi.org/10.1002/jcc.22984
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