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231224s2017 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24729
|2 doi
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|a pubmed25n0893.xml
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|a (DE-627)NLM268060428
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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 |
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|a Johnston, Travis
|e verfasserin
|4 aut
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| 245 |
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|a In situ data analytics and indexing of protein trajectories
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|c 2017
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| 336 |
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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 27.11.2019
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|a Date Revised 27.11.2019
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2017 Wiley Periodicals, Inc.
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|a The transition toward exascale computing will be accompanied by a performance dichotomy. Computational peak performance will rapidly increase; I/O performance will either grow slowly or be completely stagnant. Essentially, the rate at which data are generated will grow much faster than the rate at which data can be read from and written to the disk. MD simulations will soon face the I/O problem of efficiently writing to and reading from disk on the next generation of supercomputers. This article targets MD simulations at the exascale and proposes a novel technique for in situ data analysis and indexing of MD trajectories. Our technique maps individual trajectories' substructures (i.e., α-helices, β-strands) to metadata frame by frame. The metadata captures the conformational properties of the substructures. The ensemble of metadata can be used for automatic, strategic analysis within a trajectory or across trajectories, without manually identify those portions of trajectories in which critical changes take place. We demonstrate our technique's effectiveness by applying it to 26.3k helices and 31.2k strands from 9917 PDB proteins and by providing three empirical case studies. © 2017 Wiley Periodicals, Inc
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|a Journal Article
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| 650 |
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|a Research Support, N.I.H., Extramural
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| 650 |
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|a Research Support, Non-U.S. Gov't
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| 650 |
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4 |
|a Research Support, U.S. Gov't, Non-P.H.S.
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| 650 |
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4 |
|a conformational metadata
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| 650 |
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|a eigenvalues
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| 650 |
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|a exascale computing
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| 650 |
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4 |
|a high-performance computing
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| 650 |
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|a protein trajectories
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| 650 |
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|a Proteins
|2 NLM
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| 700 |
1 |
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|a Zhang, Boyu
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Liwo, Adam
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Crivelli, Silvia
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Taufer, Michela
|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 38(2017), 16 vom: 15. Juni, Seite 1419-1430
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
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|g volume:38
|g year:2017
|g number:16
|g day:15
|g month:06
|g pages:1419-1430
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.24729
|3 Volltext
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