NDLI: Molecular distance geometry optimization using geometric build-up and evolutionary techniques on GPU

Content Provider	IEEE Xplore Digital Library
Author	Fabry-Asztalos, L. Lorentz, I. Andonie, R.
Copyright Year	2012
Description	Author affiliation: Department of Chemistry, Central Washington University, Ellensburg, USA (Fabry-Asztalos, L.) \|\| Electronics and Computers Department, Transilvania University, Braşov, Romania (Lorentz, I.) \|\| Computer Science Department, Central Washington University, Ellensburg, USA (Andonie, R.)
Abstract	We present a combination of methods addressing the molecular distance problem, implemented on a graphic processing unit. First, we use geometric build-up and depth-first graph traversal. Next, we refine the solution by simulated annealing. For an exact but sparse distance matrix, the build-up method reconstructs the 3D structures with a root-mean-square error (RMSE) in the order of 0.1 Å. Small and medium structures (up to 10,000 atoms) are computed in less than 10 seconds. For the largest structures (up to 100,000 atoms), the build-up RMSE is 2.2 Å and execution time is about 540 seconds. The performance of our approach depends largely on the graph structure. The SA step improves accuracy of the solution to the expense of a computational overhead.
Starting Page	321
Ending Page	328
File Size	1428103
Page Count	8
File Format	PDF
ISBN	9781467311908
e-ISBN	9781467311915
DOI	10.1109/CIBCB.2012.6217247
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-05-09
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Complexity theory Simulated annealing Proteins Vectors Geometry Graphics processing unit Chemicals Graph algorithms Graphics processors Molecular Distance Geometry Parallel algorithms
Content Type	Text
Resource Type	Article

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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