Ranking beta sheet topologies of proteins

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

Standard

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

Harvard

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>

APA

Fonseca, R., Helles, G., & Winter, P. (2010). Ranking beta sheet topologies of proteins. In S. I. Ao, C. Douglas, W. S. Grundfest, & J. Burgstone (Eds.), Proceedings of the World Congress on Engineering and Computer Science 2010 (Vol. 2, pp. 624-628). Newswood Limited. http://www.iaeng.org/publication/WCECS2010/WCECS2010_pp624-628.pdf

Vancouver

Fonseca R, Helles G, Winter P. Ranking beta sheet topologies of proteins. In Ao SI, Douglas C, Grundfest WS, Burgstone J, editors, Proceedings of the World Congress on Engineering and Computer Science 2010. Vol. 2. Newswood Limited. 2010. p. 624-628

Author

Fonseca, Rasmus ; Helles, Glennie ; Winter, Pawel. / Ranking beta sheet topologies of proteins. Proceedings of the World Congress on Engineering and Computer Science 2010. editor / S. I. Ao ; Craig Douglas ; W. S. Grundfest ; Jon Burgstone. Vol. 2 Newswood Limited, 2010. pp. 624-628

Bibtex

@inproceedings{3cdd9ae05da411df928f000ea68e967b,
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.",
keywords = "Faculty of Science, protein, bioinformatik, protein, bioinformatics",
author = "Rasmus Fonseca and Glennie Helles and Pawel Winter",
year = "2010",
language = "English",
isbn = "978-988-18210-0-3",
volume = "2",
pages = "624--628",
editor = "Ao, {S. I.} and Craig Douglas and Grundfest, {W. S.} and Jon Burgstone",
booktitle = "Proceedings of the World Congress on Engineering and Computer Science 2010",
publisher = "Newswood Limited",
note = "null ; Conference date: 20-10-2010 Through 22-10-2010",

}

RIS

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

Y2 - 20 October 2010 through 22 October 2010

ER -

ID: 19709951