Characterizing Protein Conformation Space
Author(s)Nigham, Anshul; Hsu, David; Latombe, Jean-Claude
In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms are not in self-collision. Unlike energy based methods, this approach allows efficient exploration and remains general -- the benefits of characterization of the space apply to all proteins. We hypothesize that this conformation space branches into many small funnels as we sample compact conformations. We develop a compact representation the conformation space, and give experimental results that support our hypothesis. Potential applications of our method include protein folding as well as observing structural relationships between proteins.
Computer Science (CS)
Protein Structure, Protein Conformation Space, Protein Folding