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Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

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Gao Z., Rostami R., Pang X., Fu Z., Yu Z.
Molecular Based Mathematical Biology
|
2016
|
tom 4
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nr 1
EN
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 descriptor is applied to shape comparison between molecules with deformed structures. The proposed methods are implemented into a program that can be used as a stand-alone software tool or as a plug-in to other existing molecular modeling tools. Particularly, the code is encapsulated into a software toolkit with a user-friendly graphical interface developed by the authors.
2
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SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

100%
Jiang Y., Xie Y., Ying J., Xie D., Yu Z.
Molecular Based Mathematical Biology
|
2015
|
tom 3
|
nr 1
EN
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 of a biomolecule, and to calculate PBE solutions in a remote and user friendly fashion. The web server is available on the website https://lsextrnprod.uwm.edu/electrostatics/.
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