Kavraki Lab
A. Novinskaya, D. Devaurs, M. Moll, and L. E. Kavraki, “Defining Low-Dimensional Projections to Guide Protein Conformational Sampling,” Journal of Computational Biology, vol. 24, no. 1, pp. 79–89, Jan. 2017.

Abstract

Exploring the conformational space of proteins is critical to characterizing their functions. Numerous methods have been proposed to sample a protein’s conformational space, including techniques developed in the field of robotics and known as sampling-based motion-planning algorithms (or sampling-based planners). However, these algorithms suffer from the curse of dimensionality when applied to large pro- teins. Many sampling-based planners attempt to mitigate this issue by keeping track of sampling density to guide conformational sampling toward unexplored regions of the conformational space. This is often done using low-dimensional projections as an indirect way to reduce the dimensionality of the exploration problem. However, how to choose an appropriate projection and how much it influences the planner’s performance are still poorly understood problems. In this paper, we introduce two methodologies defining low-dimensional projections that can be used by sampling-based planners for protein conformational sampling. The first method leverages information about a protein’s flexibility to construct projections that can efficiently guide conformational sampling, when expert knowledge is available. The second method builds similar projections automatically, without expert intervention. We evaluate the projections produced by both methodologies on two conformational-search problems involving three middle-size proteins. Our experiments demonstrate that (i) defining projections based on expert knowledge can benefit conformational sampling, and (ii) automatically constructing such projections is a reasonable alternative.

Publisher: http://dx.doi.org/10.1089/cmb.2016.0144

PDF preprint: http://kavrakilab.org/publications/novinskaya2016_defining_proj.pdf