Efficient algorithms to explore conformation spaces of flexible protein loops

Authors:
Ankur Dhanik;Peggy Yao;Nathan Marz;Ryan Propper;Charles Kou;Guanfeng Liu;Henry van den Bedem;Jean-Claude Latombe
Affiliations:
Computer Science Department, Stanford University, Stanford, CA;Computer Science Department, Stanford University, Stanford, CA;Computer Science Department, Stanford University, Stanford, CA;Computer Science Department, Stanford University, Stanford, CA;Computer Science Department, Stanford University, Stanford, CA;Computer Science Department, Stanford University, Stanford, CA;Joint Center for Structural Genomics, SLAC, Menlo Park, CA;Computer Science Department, Stanford University, Stanford, CA
Venue:
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Year:
2007

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Abstract

Two efficient and complementary sampling algorithms are presented to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples conformations broadly distributed over this space, while the "deformation sampling" algorithm uses these conformations as starting points to explore more finely selected regions of the space. Computational results are shown for loops ranging from 5 to 25 residues. The algorithms are implemented in a toolkit, LoopTK, available at https://simtk.org/home/looptk.