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231224s2013 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.23110
|2 doi
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|a pubmed24n0737.xml
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|a (DE-627)NLM221193367
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|a (NLM)22996151
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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 Zhao, Yutong
|e verfasserin
|4 aut
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| 245 |
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|a A fast parallel clustering algorithm for molecular simulation trajectories
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|c 2013
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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
|b cr
|2 rdacarrier
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|a Date Completed 29.04.2013
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|a Date Revised 04.12.2012
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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 implemented a GPU-powered parallel k-centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than the CPU implementation. We tested our algorithm on four protein MD simulation datasets ranging from the small Alanine Dipeptide to a 370-residue Maltose Binding Protein (MBP). It is capable of grouping 250,000 conformations of the MBP into 4000 clusters within 40 seconds. To achieve this, we effectively parallelized the code on the GPU and utilize the triangle inequality of metric spaces. Furthermore, the algorithm's running time is linear with respect to the number of cluster centers. In addition, we found the triangle inequality to be less effective in higher dimensions and provide a mathematical rationale. Finally, using Alanine Dipeptide as an example, we show a strong correlation between cluster populations resulting from the k-centers algorithm and the underlying density. © 2012 Wiley Periodicals, Inc
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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, Non-U.S. Gov't
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|a Dipeptides
|2 NLM
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|a Escherichia coli Proteins
|2 NLM
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|a Islet Amyloid Polypeptide
|2 NLM
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|a Maltose-Binding Proteins
|2 NLM
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|a Proteins
|2 NLM
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|a Trpzip2 protein
|2 NLM
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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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| 700 |
1 |
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|a Sheong, Fu Kit
|e verfasserin
|4 aut
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| 700 |
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|a Sun, Jian
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Sander, Pedro
|e verfasserin
|4 aut
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| 700 |
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|a Huang, Xuhui
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 34(2013), 2 vom: 15. Jan., Seite 95-104
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
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|g volume:34
|g year:2013
|g number:2
|g day:15
|g month:01
|g pages:95-104
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|u http://dx.doi.org/10.1002/jcc.23110
|3 Volltext
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