Adaptive local learning in sampling based motion planning for protein folding
Abstract
Background: Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. Probabilistic Roadmap Methods and variants contain several phases (i.e., sampling, connection, and path extraction). Most of the time is spent in the connection phase and selecting which variant to employ is a difficult task. 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 develop a local learning algorithm that exploits the past performance of methods within the neighborhood of the current connection attempts 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. We compare the success rate when using our methods and other methods. We demonstrate a clear need for learning (i.e., only learning methods were able to validate against all available experimental data) and show that local learning is superior to global learning producing, in manymore »
- Authors:
-
- Texas A&M Univ., College Station, TX (United States). Dept. of Computer Science and Engineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH) National Cancer Institute (NCI)
- OSTI Identifier:
- 1626879
- Grant/Contract Number:
- AC02-05CH11231; CNS-0551685; CCF-0833199; CCF-1423111; CCF-0830753; IIS-0916053; IIS-0917266; EFRI-1240483; RI-1217991; R25 CA090301-11
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Systems Biology
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: S2; Journal ID: ISSN 1752-0509
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- Mathematical & Computational Biology
Citation Formats
Ekenna, Chinwe, Thomas, Shawna, and Amato, Nancy M. Adaptive local learning in sampling based motion planning for protein folding. United States: N. p., 2016.
Web. doi:10.1186/s12918-016-0297-9.
Ekenna, Chinwe, Thomas, Shawna, & Amato, Nancy M. Adaptive local learning in sampling based motion planning for protein folding. United States. https://doi.org/10.1186/s12918-016-0297-9
Ekenna, Chinwe, Thomas, Shawna, and Amato, Nancy M. Mon .
"Adaptive local learning in sampling based motion planning for protein folding". United States. https://doi.org/10.1186/s12918-016-0297-9. https://www.osti.gov/servlets/purl/1626879.
@article{osti_1626879,
title = {Adaptive local learning in sampling based motion planning for protein folding},
author = {Ekenna, Chinwe and Thomas, Shawna and Amato, Nancy M.},
abstractNote = {Background: Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. Probabilistic Roadmap Methods and variants contain several phases (i.e., sampling, connection, and path extraction). Most of the time is spent in the connection phase and selecting which variant to employ is a difficult task. 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 develop a local learning algorithm that exploits the past performance of methods within the neighborhood of the current connection attempts 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. We compare the success rate when using our methods and other methods. We demonstrate a clear need for learning (i.e., only learning methods were able to validate against all available experimental data) and show that local learning is superior to global learning producing, in many cases, significantly higher quality results than the other methods. Conclusions: We present an algorithm that uses local learning to select appropriate connection methods in the context of roadmap construction for protein folding. Our method removes the burden of deciding which method to use, leverages the strengths of the individual input methods, and it is extendable to include other future connection methods.},
doi = {10.1186/s12918-016-0297-9},
journal = {BMC Systems Biology},
number = S2,
volume = 10,
place = {United States},
year = {Mon Aug 01 00:00:00 EDT 2016},
month = {Mon Aug 01 00:00:00 EDT 2016}
}
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