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231224s2015 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.23948
|2 doi
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|a pubmed24n0832.xml
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|a DE-627
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|e rakwb
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|a eng
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| 100 |
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|a Higo, Junichi
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking
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|c 2015
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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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|a Date Completed 04.04.2016
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|a Date Revised 27.06.2015
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2015 Wiley Periodicals, Inc.
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|a A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did
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|a Journal Article
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|a Research Support, Non-U.S. Gov't
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|a adaptive umbrella
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|a flexible docking
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|a free-energy landscape
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|a multicanonical
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|a virtual system
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|a Amyloid beta-Peptides
|2 NLM
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| 700 |
1 |
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|a Dasgupta, Bhaskar
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Mashimo, Tadaaki
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Kasahara, Kota
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Fukunishi, Yoshifumi
|e verfasserin
|4 aut
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| 700 |
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|a Nakamura, Haruki
|e verfasserin
|4 aut
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| 773 |
0 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 36(2015), 20 vom: 30. Juli, Seite 1489-501
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
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|g volume:36
|g year:2015
|g number:20
|g day:30
|g month:07
|g pages:1489-501
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|u http://dx.doi.org/10.1002/jcc.23948
|3 Volltext
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