article

Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials

Authors:

Afra Zomorodian,

Leonidas Guibas,

Patrice KoehlAuthors Info & Claims

Computer Aided Geometric Design, Volume 23, Issue 6

Pages 531 - 544

Published: 01 August 2006 Publication History

Abstract

Distance-dependent, pairwise, statistical potentials are based on the concept that the packing observed in known protein structures can be used as a reference for comparing different 3D models for a protein. Here, packing refers to the set of all pairs of atoms in the molecule. Among all methods developed to assess three-dimensional models, statistical potentials are subject both to praise for their power of discrimination, and to criticism for the weaknesses of their theoretical foundations. Classical derivations of pairwise potentials assume statistical independence of all pairs of atoms. This assumption, however, is not valid in general. We show that we can filter the list of all interactions in a protein to generate a much smaller subset of pairs that retains most of the structural information contained in proteins. The filter is based on a geometric method called alpha shapes that captures the packing in a conformation. Statistical scoring functions derived from such subsets perform as well as scoring functions derived from the set of all pairwise interactions.

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Cited By

Varytimidis CRapantzikos KAvrithis YKollias S(2018)α-shapes for local feature detectionPattern Recognition10.1016/j.patcog.2015.08.01650:C(56-73)Online publication date: 30-Dec-2018
https://dl.acm.org/doi/10.1016/j.patcog.2015.08.016
Varytimidis CRapantzikos KAvrithis Y(2012)WαSHProceedings, Part II, of the 12th European Conference on Computer Vision --- ECCV 2012 - Volume 757310.5555/2964398.2964457(788-801)Online publication date: 7-Oct-2012
https://dl.acm.org/doi/10.5555/2964398.2964457

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Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials

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Published In

cover image Computer Aided Geometric Design

Computer Aided Geometric Design Volume 23, Issue 6

Special issue: Applications of geometric modeling in the life sciences

August 2006

79 pages

ISSN:0167-8396

Issue’s Table of Contents

Copyright © Elsevier B.V. © 2006.

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Elsevier Science Publishers B. V.

Netherlands

Publication History

Published: 01 August 2006

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Cited By

Varytimidis CRapantzikos KAvrithis YKollias S(2018)α-shapes for local feature detectionPattern Recognition10.1016/j.patcog.2015.08.01650:C(56-73)Online publication date: 30-Dec-2018
https://dl.acm.org/doi/10.1016/j.patcog.2015.08.016
Varytimidis CRapantzikos KAvrithis Y(2012)WαSHProceedings, Part II, of the 12th European Conference on Computer Vision --- ECCV 2012 - Volume 757310.5555/2964398.2964457(788-801)Online publication date: 7-Oct-2012
https://dl.acm.org/doi/10.5555/2964398.2964457

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