title: Information theoretical measures to analyze trajectories in rational molecular design.
abstract: We develop a new methodology to analyze molecular dynamics trajectories and other time series data from simulation runs. This methodology is based on an information measure of the difference between distributions of various data extract from such simulations. The method is fast as it only involves the numerical integration/summation of the distributions in one dimension while avoiding sampling issues at the same time. The method is most suitable for applications in which different scenarios are to be compared, e.g. to guide rational molecular design. We show the power of the proposed method in an application of rational drug design by reduced model computations on the BH3 motif in the apoptosis inducing BCL(2) protein family.
authors.affiliation: Max-Planck-Institute for the Physics of Complex Systems, Nöthnitzerstrasse 38, Dresden, Germany. hamacher@pks.mpg.de
authors.forename: K
authors.initials: K
authors.lastname: Hamacher
mesh_terms: D003198:Computer Simulation; D015195:Drug Design; D007257:Information Theory; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D011518:Proto-Oncogene Proteins / Q000737:chemistry*
chemical_list: C474007:Bax protein (53-86); D010446:Peptide Fragments; D011518:Proto-Oncogene Proteins