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SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

Yi Jiang;  Yang Xie;  Jinyong Ying;  Dexuan Xie;  Zeyun Yu — 2015

Molecular Based Mathematical Biology

The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present an SDPBS web server in this paper that allows clients to visualize and manipulate the molecular structure...

Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

Zhanheng Gao;  Reihaneh Rostami;  Xiaoli Pang;  Zhicheng Fu;  Zeyun Yu — 2016

Molecular Based Mathematical Biology

Novel approaches for generating and comparing flexible (non-rigid) molecular surface meshes are developed. The mesh-generating method is fast and memory-efficient. The resulting meshes are smooth and accurate, and possess high mesh quality. An isometric-invariant shape descriptor based on the Laplace- Beltrami operator is then explored for mesh comparing. The new shape descriptor is more powerful in discriminating different surface shapes but rely only on a small set of signature values. The shape...

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