Optimization of Gaussian surface calculations and extension to solvent-accessible surface areas

Weiser, Jörg; Shenkin, Peter S.; Still, W. Clark

doi:10.1002/(sici)1096-987x(199905)20:7<688::aid-jcc4>3.0.co;2-f

Cited by 56 publications

(50 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The VDW surface, SAS and SES can be approximated well by the Gaussian surface with proper parameter selection [6,7]. The Gaussian surface has been widely used in many problems in computational biology, such as docking problem [8], molecular shape comparison [9], calculating SAS area [10] and the generalized Born models [11]. With various definitions of molecular surface that has been proposed, numerous works have been devoted to the computation of molecular surface.…”

Section: Some Definitions and Meshing Methods For Molecular Surfacementioning

confidence: 99%

Advances in biomolecular surface meshing and its applications to mathematical modeling

Chen

2013

Chin. Sci. Bull.

View full text Add to dashboard Cite

In the field of molecular modeling and simulation, molecular surface meshes are necessary for many problems, such as molecular structure visualization and analysis, docking problem and implicit solvent modeling and simulation. Recently, with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation, providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure. In this review, we summarize recent works on this issue. First, various definitions of molecular surfaces and corresponding meshing methods are introduced. Second, our recent meshing tool, TMSmesh, and its performances are presented. Finally, we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM). molecular surface meshing, manifold mesh, mathematical modeling, TMSmeshCitation: Chen M X, Lu B Z. Advances in biomolecular surface meshing and its applications to mathematical modeling. Chin Sci Bull, 2013Bull, , 58: 1843Bull, -1849 10.1007/s11434-013-5829-8One main goal of computational structural biology/chemistry is to understand the functions and mechanisms of biomolecular systems and their relations to molecular structures with a wide range of computational approaches. To achieve this, proper and correct representation of the interface between biomolecule and solvent, molecular surface, is a primary task. In the field of implicit solvent modeling and continuum modeling, the molecular surface is used to model the dielectric interface which is the transition from the low-dielectric solute region to the high-dielectric solvent region. It is also important and useful in materials science and surface science [1]. Meshing molecular surface is a prerequisite for using boundary element method (BEM) and finite element method (FEM) in the implicit solvent models, and it is a more demanding task than for the only purposes of visualization and/or geometry analyses of molecular structure. So far, due to the highly complex and irregular shape of the molecular surface, *Corresponding author (email: bzlu@lsec.cc.ac.cn) efficient meshing of molecular surface for large real biomolecule with high quality remains a challenging problem. Actually, it was historically a great impediment to use BEM/FEM in continuum modeling of large molecular systems.The main purpose of this paper is to review the various definitions and meshing methods for molecular surface, including our recent work, and introduce their applications in implicit solvent modeling and simulation. Following this introduction section, in Section 1, various definitions of molecular surfaces and corresponding meshing methods are introduced. In Section 2, our recent algorithm and software, TMSmesh, are focused. We also made comparisons with some other methods. In Section 3, a closely related topic, volume me...

show abstract

Section: Some Definitions and Meshing Methods For Molecular Surfacementioning

confidence: 99%

Advances in biomolecular surface meshing and its applications to mathematical modeling

Chen

2013

Chin. Sci. Bull.

View full text Add to dashboard Cite

show abstract

“…The VDW surface, SAS and SES can be approximated well by the Gaussian surface with proper parameter selection [25,26]. The Gaussian surface has been widely used in many problems in computational biology, such as docking problem [27], molecular shape comparison [28], calculating SAS area [29] and the generalized Born models [30]. TMSmesh contains two main steps.…”

Section: Previous Algorithms In Tmsmeshmentioning

confidence: 99%

Triangulated manifold meshing method preserving molecular surface topology

Chen

2012

Journal of Molecular Graphics and Modelling

View full text Add to dashboard Cite

“…Molecular surfaces can be represented analytically as a patch complex of spheres (van der Walls surfaces and Lee-Richards surfaces) [29,24] or as a patch complex of spheres and tori (Connolly surfaces) [14,36] or as a patch complex of spheres and quadratic hyperboloids [17] or as parametric B-spline or NURBs surfaces [2,3] or as level sets resulting from summing up Gaussian atomic electron density functions (Gaussian surfaces) [7,9,16,22,46] or implicit algebraic splines or A-patch surfaces [50]. Of course, linear surface tessellations can be generated from those analytical forms of molecular surfaces [15,42,1,13,28,49,35,37].…”

Section: Related Workmentioning

confidence: 99%