Adaptive local learning in sampling based motion planning for protein folding

Chinwe Ekenna, Shawna Thomas, Nancy M. Amato

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

Abstract

Motivation: Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms such as Probabilistic Roadmap Methods (PRMs) have been successful in modeling the protein folding landscape. PRMs and variants contain several phases (i.e., sampling, connection, and path extraction). Global machine learning has been applied to the connection phase but is inefficient in situations with varying topology, such as those typical of folding landscapes. Results: We present a local learning algorithm that considers the past performance near the current connection attempt as a basis for learning. It is sensitive not only to different types of landscapes but also to differing regions in the landscape itself, removing the need to explicitly partition the landscape. We perform experiments on 23 proteins of varying secondary structure makeup with 52-114 residues. Our method models the landscape with better quality and comparable time to the best performing individual method and to global learning.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages61-68
Number of pages8
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
Externally publishedYes
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Conference

ConferenceIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

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