Efficient algorithms to explore conformation spaces of flexible protein loops

A. Dhanik, P. Yao, N. Marz, R. Propper, C. Kou, Guanfeng Liu, H. Van Den Bedem, J. C. Latombe

Research output: Chapter in Book/Report/Conference proceedingConference proceeding contribution

4 Citations (Scopus)

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.
Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Place of PublicationLos Alamitos, CA
PublisherSpringer, Springer Nature
Pages265-276
Number of pages12
ISBN (Print)9783540741251
DOIs
Publication statusPublished - 2007
Externally publishedYes
EventInternational Workshop on Algorithms in Bioinformatics - Philadelphia, PA
Duration: 8 Sep 20079 Sep 2007

Workshop

WorkshopInternational Workshop on Algorithms in Bioinformatics
CityPhiladelphia, PA
Period8/09/079/09/07

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