Identification of Metastabilities in Monomolecular Conformation Kinetics

摘要: The identification of metastable conformations molecules plays an important role in computational drug design. One main difficulty is the fact that underlying dynamic processes take place high dimensional spaces. Although restriction degrees freedom to a few dihedral angles significantly reduces complexity problem, existing algorithms are time-consuming. They mainly based on approximation of transfer operator by extensive sampling states according to Boltzmann distribution and short-time Hamiltonian dynamics simulations. We present method which can identify without complete distribution. Our algorithm on local transition rates uses only pointwise information about potential energy surface. In order apply cluster PCCA+, we compute eigenvectors rate matrix Jacobi-Davidson method. Interpolation techniques applied approximate thermodynamical weights clusters. concluding example illustrates our approach for epigallocatechine, molecule be described seven angles.