http://www.cnr.it/ontology/cnr/individuo/prodotto/ID266143
CUDA accelerated molecular surface generation (Articolo in rivista)
- Type
- Label
- CUDA accelerated molecular surface generation (Articolo in rivista) (literal)
- Anno
- 2014-01-01T00:00:00+01:00 (literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
- 10.1002/cpe.3120 (literal)
- Alternative label
Daniele D'Agostino, Andrea Clematis , Sergio Decherchi , Walter Rocchia , Luciano Milanesi and Ivan Merelli (2014)
CUDA accelerated molecular surface generation
in Concurrency and computation; John Wiley & Sons Ltd., Chichester (Regno Unito)
(literal)
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- Daniele D'Agostino, Andrea Clematis , Sergio Decherchi , Walter Rocchia , Luciano Milanesi and Ivan Merelli (literal)
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- Special Issue on COMPBIO 2013
First published online 15/8/2013 (literal)
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- ISI Web of Science (WOS) (literal)
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- Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy
Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, Genoa, Italy
Institute for Biomedical Technologies, National Research Council of Italy, Segrate, Milan, Italy (literal)
- Titolo
- CUDA accelerated molecular surface generation (literal)
- Abstract
- A proper and efficient representation of possibly complex and large molecular surfaces is an important task
in bioinformatics and biophysics. Molecular surfaces indeed are used for different aims, in particular, for
computation, as visual support tools for biologists, in electrostatics problems involving implicit solvents
(e.g. while solving the Poisson-Boltzmann equation) or for molecular dynamics simulations. This is the reason
why, in literature, a multitude of algorithms that differ on the basis of the adopted representation and the
approach/technology used were proposed. In this paper we present a CUDA-based software component able
to produce high-resolution molecular surfaces based on the Van der Waals, solvent accessible, Richards-
Connolly and blobby definitions. The component was designed to be used in heterogeneous visualization
pipelines; therefore, the representation of the molecular surfaces suits both the direct visualization and the
efficient storing for following processing steps. Experimental results show speedup figures between 39.3
and 88.4 considering molecules of different sizes and surface resolutions, resulting in meshes of up to 258.6
million triangles. (literal)
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