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Authors: Pawel Winter and Rasmus Fonseca

Affiliation: University of Copenhagen, Denmark

ISBN: 978-989-758-070-3

ISSN: 2184-4305

Keyword(s): Protein Structure Prediction, Force Field, Alpha-complexes, Kinetic Data Structures.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Structure Prediction

Abstract: Reducing the computational effort and increasing the accuracy of potential energy functions is of utmost importance in modeling biological systems, for instance in protein structure prediction, docking or design. Evaluating interactions between nonbonded atoms is the bottleneck of such computations. It is shown that local properties of a-complexes (subcomplexes of Delaunay tessellations) make it possible to identify nonbonded pairs of atoms whose contributions to the potential energy are not marginal and cannot be disregarded. Computational experiments indicate that using the local properties of a-complexes, the relative error (when compared to the potential energy contributions of all nonbonded pairs of atom) is well within 2%. Furthermore, the computational effort (assuming that a-complexes are given) is comparable to even the simplest and therefore also fastest cutoff approaches. The determination of a-complexes from scratch for every configuration encountered during the search fo r the native structure would make this approach hopelessly slow. However, it is argued that kinetic a-complexes can be used to reduce the computational effort of determining the potential energy when ``moving" from one configuration to a neighboring one. As a consequence, relatively expensive (initial) construction of an a-complex is expected to be compensated by subsequent fast kinetic updates during the search process. Computational results presented in this paper are limited. However, they suggest that the applicability of a-complexes and kinetic a-complexes in protein related problems (e.g., protein structure prediction and protein-ligand docking) deserves furhter investigation. (More)


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Paper citation in several formats:
Winter, P. and Fonseca, R. (2015). Alpha Complexes in Protein Structure Prediction. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3 ISSN 2184-4305, pages 178-182. DOI: 10.5220/0005251401780182

author={Pawel Winter. and Rasmus Fonseca.},
title={Alpha Complexes in Protein Structure Prediction},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2015)},


JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2015)
TI - Alpha Complexes in Protein Structure Prediction
SN - 978-989-758-070-3
IS - 2184-4305
AU - Winter, P.
AU - Fonseca, R.
PY - 2015
SP - 178
EP - 182
DO - 10.5220/0005251401780182

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