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 -