Ranking beta sheet topologies of proteins
Publikation: Bidrag til bog/antologi/rapport › Konferencebidrag i proceedings › Forskning › fagfællebedømt
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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. red. / S. I. Ao; Craig Douglas; W. S. Grundfest; Jon Burgstone. Bind 2 Newswood Limited, 2010. s. 624-628.Publikation: Bidrag til bog/antologi/rapport › Konferencebidrag i proceedings › Forskning › fagfællebedømt
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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
Y2 - 20 October 2010 through 22 October 2010
ER -
ID: 19709951