A Fast Variational Method for the Construction of Resolution Adaptive C-Smooth Molecular Surfaces.

ABSTRACT: We present a variational approach to smooth molecular (proteins, nucleic acids) surface constructions, starting from atomic coordinates, as available from the protein and nucleic-acid data banks. Molecular dynamics (MD) simulations traditionally used in understanding protein and nucleic-acid folding processes, are based on molecular force fields, and require smooth models of these molecular surfaces. To accelerate MD simulations, a popular methodology is to employ coarse grained molecular models, which represent clusters of atoms with similar physical properties by psuedo- atoms, resulting in coarser resolution molecular surfaces. We consider generation of these mixed-resolution or adaptive molecular surfaces. Our approach starts from deriving a general form second order geometric partial

SUBMITTER: Bajaj CL 

PROVIDER: S-EPMC2755577 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature