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231223s2009 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.21337
|2 doi
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|a pubmed24n1620.xml
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|a (DE-627)NLM189111658
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|a (NLM)19504588
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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| 100 |
1 |
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|a Zhang, Xin
|e verfasserin
|4 aut
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| 245 |
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|a Absolute free energies estimated by combining precalculated molecular fragment libraries
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|c 2009
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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 30.09.2009
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|a Date Revised 04.12.2024
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|a published: Print
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|a Citation Status MEDLINE
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| 520 |
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|a 2009 Wiley Periodicals, Inc.
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|a The absolute free energy--or partition function, equivalently--of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by precalculating fragment configurations and interactions for reuse in a variety of molecules. We use such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost and are used to check our results by comparison to standard dynamics simulation. We explain how our work can be extended to estimate relative binding affinities
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|a Journal Article
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|a Research Support, N.I.H., Extramural
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|a Research Support, U.S. Gov't, Non-P.H.S.
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| 650 |
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|a Dipeptides
|2 NLM
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| 650 |
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|a Oligopeptides
|2 NLM
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| 650 |
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|a Polymers
|2 NLM
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| 650 |
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|a alanylalanine
|2 NLM
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| 650 |
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|a 2867-20-1
|2 NLM
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| 650 |
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|a alanyl-alanyl-alanyl-alanine
|2 NLM
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| 650 |
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|a 926-79-4
|2 NLM
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| 700 |
1 |
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|a Mamonov, Artem B
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Zuckerman, Daniel M
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 30(2009), 11 vom: 31. Aug., Seite 1680-91
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:30
|g year:2009
|g number:11
|g day:31
|g month:08
|g pages:1680-91
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.21337
|3 Volltext
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