Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.

ABSTRACT: Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaus-sian kernel functions is employed to generate implicit models for biomolecules. The coefficients in the summation are designed as functions of the structure indices, which specify the structures at a certain level and enable a local resolution control on the biomolecular surface. A method called neighboring search is adopted to locate the grid points close to the expected biomolecu

SUBMITTER: Liao T 

PROVIDER: S-EPMC3858848 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature