GPU Accelerated Molecular Surface Computing

A method is presented for computing the SES (solvent excluded surface) of a protein molecule in interactive-time based on GPU (graphics processing unit) acceleration. First, the offset surface of the van der Waals spheres is sampled using an offset distance d that corresponds to the radius of the solvent probe. The SES is then constructed by extracting the surface at distance d from the sample points. For interactive-time computing, two space partitioning schemes are used, a voxel map and kd-tree, with data parallel schemes accelerated by GPU. In experiments using an average 1,848 atoms, a SES with a resolution of 1/2 7 ×1/2 7 × 1/2 7 of the original bounding box is obtained in 66.53ms on average.

[1]  Thomas Ertl,et al.  Interactive Visualization of Molecular Surface Dynamics , 2009, IEEE Transactions on Visualization and Computer Graphics.

[2]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[3]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[4]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[5]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[6]  A. Bondi.  van der Waals Volumes and Radii , 1964 .

[7]  Daniel Baum,et al.  Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Accelerated Visualization of Dynamic Molecular Surfaces , 2022 .

[8]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[9]  Yuan-Fang Wang,et al.  Efficient molecular surface generation using level-set methods. , 2006, Journal of molecular graphics & modelling.

[10]  Abel J. P. Gomes,et al.  Graphics processing unit‐based triangulations of Blinn molecular surfaces , 2011, Concurr. Comput. Pract. Exp..

[11]  William E. Lorensen,et al.  Marching cubes: A high resolution 3D surface construction algorithm , 1987, SIGGRAPH.

[12]  Dinesh Manocha,et al.  DiFi: Fast 3D Distance Field Computation Using Graphics Hardware , 2004, Comput. Graph. Forum.

[13]  R Abagyan,et al.  The contour-buildup algorithm to calculate the analytical molecular surface. , 1996, Journal of structural biology.

[14]  Amitabh Varshney,et al.  Parallel, stochastic measurement of molecular surface area. , 2008, Journal of molecular graphics & modelling.

[15]  Deok-Soo Kim,et al.  Molecular surfaces on proteins via beta shapes , 2007, Comput. Aided Des..

[16]  Dinesh Manocha,et al.  Interactive 3D distance field computation using linear factorization , 2006, I3D '06.

[17]  Matthieu Chavent,et al.  MetaMol: high-quality visualization of molecular skin surface. , 2008, Journal of molecular graphics & modelling.

[18]  Chang-Hun Kim,et al.  CUDA-based Signed Distance Field Calculation for Adaptive Grids , 2010, 2010 10th IEEE International Conference on Computer and Information Technology.

[19]  Jakob Andreas Bærentzen,et al.  3D distance fields: a survey of techniques and applications , 2006, IEEE Transactions on Visualization and Computer Graphics.