Efficient algorithms to explore conformation spaces of flexible protein loops.

ABSTRACT: Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free confor

SUBMITTER: Yao P 

PROVIDER: S-EPMC2794838 | biostudies-literature | 2008 Oct-Dec

REPOSITORIES: biostudies-literature