Ranking beta sheet topologies of proteins

Rasmus Fonseca; Glennie Helles; Pawel Winter

Ranking beta sheet topologies of proteins

Rasmus Fonseca, Glennie Helles, Pawel Winter

Department of Computer Science

Abstract

One of the challenges of protein structure prediction is to identify long-range interactions between amino acids. To reliably predict such interactions, we enumerate, score and rank all beta-topologies (partitions of beta-strands into sheets, orderings of strands within sheets and orientations of paired strands) of a given protein. We show that the beta-topology corresponding to the native structure is, with high probability, among the top-ranked. Since full enumeration is very time-consuming, we also suggest a method to deal with proteins with many beta-strands.
The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. The top-ranked beta-topologies can be used to find initial conformations from which conformational searches can be started. They can also be used to filter decoys by removing those with poorly assembled beta-sheets, and finally they can be relevant in contact prediction methods.

Original language	English
Title of host publication	Proceedings of the World Congress on Engineering and Computer Science 2010
Editors	S. I. Ao, Craig Douglas, W. S. Grundfest, Jon Burgstone
Number of pages	5
Volume	2
Publisher	Newswood Limited
Publication date	2010
Pages	624-628
ISBN (Print)	978-988-18210-0-3
Publication status	Published - 2010
Event	World Congress on Engineering and Computer Science 2010 (WCECS) - San Francisco, United States Duration: 20 Oct 2010 → 22 Oct 2010

Conference

Conference	World Congress on Engineering and Computer Science 2010 (WCECS)
Country/Territory	United States
City	San Francisco
Period	20/10/2010 → 22/10/2010

Keywords

Faculty of Science
protein
bioinformatics

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Ranking beta sheet topologies of proteins. / Fonseca, Rasmus; Helles, Glennie; Winter, Pawel.

Proceedings of the World Congress on Engineering and Computer Science 2010. ed. / S. I. Ao; Craig Douglas; W. S. Grundfest; Jon Burgstone. Vol. 2 Newswood Limited, 2010. p. 624-628.

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Fonseca, R, Helles, G & Winter, P 2010, Ranking beta sheet topologies of proteins. in SI Ao, C Douglas, WS Grundfest & J Burgstone (eds), Proceedings of the World Congress on Engineering and Computer Science 2010. vol. 2, Newswood Limited, pp. 624-628, World Congress on Engineering and Computer Science 2010 (WCECS), San Francisco, United States, 20/10/2010. <http://www.iaeng.org/publication/WCECS2010/WCECS2010_pp624-628.pdf>

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title = "Ranking beta sheet topologies of proteins",

abstract = "One of the challenges of protein structure prediction is to identify long-range interactions between amino acids. To reliably predict such interactions, we enumerate, score and rank all beta-topologies (partitions of beta-strands into sheets, orderings of strands within sheets and orientations of paired strands) of a given protein. We show that the beta-topology corresponding to the native structure is, with high probability, among the top-ranked. Since full enumeration is very time-consuming, we also suggest a method to deal with proteins with many beta-strands.The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. The top-ranked beta-topologies can be used to find initial conformations from which conformational searches can be started. They can also be used to filter decoys by removing those with poorly assembled beta-sheets, and finally they can be relevant in contact prediction methods.",

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booktitle = "Proceedings of the World Congress on Engineering and Computer Science 2010",

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note = "World Congress on Engineering and Computer Science 2010 (WCECS) ; Conference date: 20-10-2010 Through 22-10-2010",

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TY - GEN

T1 - Ranking beta sheet topologies of proteins

AU - Fonseca, Rasmus

AU - Helles, Glennie

AU - Winter, Pawel

PY - 2010

Y1 - 2010

N2 - One of the challenges of protein structure prediction is to identify long-range interactions between amino acids. To reliably predict such interactions, we enumerate, score and rank all beta-topologies (partitions of beta-strands into sheets, orderings of strands within sheets and orientations of paired strands) of a given protein. We show that the beta-topology corresponding to the native structure is, with high probability, among the top-ranked. Since full enumeration is very time-consuming, we also suggest a method to deal with proteins with many beta-strands.The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. The top-ranked beta-topologies can be used to find initial conformations from which conformational searches can be started. They can also be used to filter decoys by removing those with poorly assembled beta-sheets, and finally they can be relevant in contact prediction methods.

AB - One of the challenges of protein structure prediction is to identify long-range interactions between amino acids. To reliably predict such interactions, we enumerate, score and rank all beta-topologies (partitions of beta-strands into sheets, orderings of strands within sheets and orientations of paired strands) of a given protein. We show that the beta-topology corresponding to the native structure is, with high probability, among the top-ranked. Since full enumeration is very time-consuming, we also suggest a method to deal with proteins with many beta-strands.The results reported in this paper are highly relevant for ab initio protein structure prediction methods based on decoy generation. The top-ranked beta-topologies can be used to find initial conformations from which conformational searches can be started. They can also be used to filter decoys by removing those with poorly assembled beta-sheets, and finally they can be relevant in contact prediction methods.

KW - Faculty of Science

KW - protein

KW - bioinformatik

KW - protein

KW - bioinformatics

M3 - Article in proceedings

SN - 978-988-18210-0-3

VL - 2

SP - 624

EP - 628

BT - Proceedings of the World Congress on Engineering and Computer Science 2010

A2 - Ao, S. I.

A2 - Douglas, Craig

A2 - Grundfest, W. S.

A2 - Burgstone, Jon

PB - Newswood Limited

T2 - World Congress on Engineering and Computer Science 2010 (WCECS)

Y2 - 20 October 2010 through 22 October 2010

ER -

Ranking beta sheet topologies of proteins

Abstract

Conference

Keywords

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