Adaptive local learning in sampling based motion planning for protein folding. Issue 2 (August 2016)

• Record Type: Journal Article
• Authors: Ekenna, Chinwe; Thomas, Shawna; Amato, Nancy
• Is Part Of: BMC systems biology. Volume 10:Issue 2(2016)
• Page Start: 165
• Page End: 179
• Publication Date: 2016-08
• Subjects: Protein folding -- Motion planning -- Machine learning; Biological systems -- Periodicals; Biology -- Research -- Periodicals; Cell physiology -- Periodicals; Genes -- Analysis -- Periodicals; 571
• DOI: 10.1186/s12918-016-0297-9
• Languages: English
• ISSNs: 1752-0509

Abstract

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 alocal 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 todiffering 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 useslocal 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.