Fast Method for Computation of Channels in Dynamic Proteins

摘要

Biochemists studying the protein properties use a computer analysis of existence and proportions of the channels (cavities), leading from a biochemically significant place inside a protein to its surface. In a computer simulation and visualization, a channel in a protein can be searched as a sequence of tetrahedra in the 3D triangulation, where the protein atoms positions are used as the triangulation vertices. The geometry of a protein is not static -the atom positions change in time and biochemists have to explore a long sequence of "molecule snapshots" to find a stable channel. The recent method of a channel computation creates a triangulation of the whole protein for each snapshot.rnThe method we propose uses topology information about a channel from the previous snapshot and a clustering of atoms to cut down the number of the triangulation vertices in the current snapshot, i.e. we compute only a triangulation of an atom subset for each snapshot. Our resulting channels are almost identical with the channels computed in the triangulation of the whole protein and the total computing time falls to thirty percent and less.