Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka Michailova, Andrew D. McCulloch, Michael Holst, J. Andrew McCammon
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 […]
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Weihua Geng, Ferosh Jacob
In this paper, we present a GPU-accelerated direct-sum boundary integral method to solve the linear Poisson-Boltzmann (PB) equation. In our method, a well-posed boundary integral formulation is used to ensure the fast convergence of Krylov subspace based linear algebraic solver such as the GMRES. The molecular surfaces are discretized with flat triangles and centroid collocation. […]
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Byungjoo Kim, Ku-Jin Kim, Joon-Kyung Seong
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 […]
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Michael Krone, Sebastian Grottel, Thomas Ertl
Molecular Dynamics simulations are an essential tool for many applications. The simulation of large molecules – like proteins – over long trajectories is of high importance e. g. for pharmaceutical, biochemical and medical research. For analyzing these data sets interactive visualization plays a crucial role as details of the interactions of molecules are often affected […]
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Michael Krone, Katrin Bidmon, Thomas Ertl
Molecular dynamics simulations of proteins play a growing role in various fields such as pharmaceutical, biochemical and medical research. Accordingly, the need for high quality visualization of these protein systems raises. Highly interactive visualization techniques are especially needed for the analysis of time-dependent molecular simulations. Beside various other molecular representations the surface representations are of […]
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S. Dias, A. Gomes
The problem addressed in this paper consists in triangulating the van der Waals surface without computing the geometric intersections of its atoms. Recall that the van der Waals surface is useful in computational molecular biology and biochemistry to, for example, determine the volume occupied by a molecule, as well as other important geometric properties. Assuming […]
D. Juba, A. Varshney
Biochemists often wish to compute surface areas of proteins. A variety of algorithms have been developed for this task, but they are designed for traditional single-processor architectures. The current trend in computer hardware is towards increasingly parallel architectures for which these algorithms are not well suited. We describe a parallel, stochastic algorithm for molecular surface […]
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