895
eng
reportzib
0
2005-12-29
2005-12-29
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Identification of Metastabilities in Monomolecular Conformation Kinetics
The identification of metastable conformations of molecules plays an important role in computational drug design. One main difficulty is the fact that the underlying dynamic processes take place in high dimensional spaces. Although the restriction of degrees of freedom to a few dihedral angles significantly reduces the complexity of the problem, the existing algorithms are time-consuming. They are based on the approximation of transition probabilities by an extensive sampling of states according to the Boltzmann distribution. We present a method which can identify metastable conformations without sampling the complete distribution. Our algorithm is based on local transition rates and uses only pointwise information about the potential energy surface. In order to apply the cluster algorithm PCCA+, we compute a few eigenvectors of the rate matrix by the Jacobi-Davidson method. Interpolation techniques are applied to approximate the thermodynamical weights of the clusters. The concluding example illustrates our approach for epigallocatechine, a molecule which can be described by seven dihedral angles.
06-01
895
urn:nbn:de:0297-zib-8956
Susanna Kube
Marcus Weber
ZIB-Report
06-01
eng
uncontrolled
metastable conformations
eng
uncontrolled
potential energy surface
eng
uncontrolled
transition rates
eng
uncontrolled
eigenvectors
eng
uncontrolled
clustering
Informatik, Informationswissenschaft, allgemeine Werke
Eigenvalues, eigenvectors
Chemical kinetics [See also 76V05, 92C45, 92E20]
Random walks, random surfaces, lattice animals, etc. [See also 60G50, 82C41]
Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
ZIB Allgemein
RĂ¶blitz, Susanna
Weber, Marcus
https://opus4.kobv.de/opus4-zib/files/895/ZR-06-01.pdf