Quantitative analysis of molecular surface based on improved Marching Tetrahedra algorithm

We presented a simple and efficient method to eliminate redundant vertices produced by standard Marching Tetrahedra approach. More than 60% of time cost in quantitative analysis of molecular surface of electrostatic potential can be saved without evident deterioration of accuracy of the results. [Di...

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Bibliographic Details
Published in:Journal of molecular graphics & modelling 2012-09, Vol.38, p.314-323
Main Authors: Lu, Tian, Chen, Feiwu
Format: Article
Language:English
Subjects:
Algorithms
Average local ionization energy
Binding Sites
Computer Graphics
Computer Simulation
Electrostatic potential
Imaging, Three-Dimensional - economics
Imaging, Three-Dimensional - methods
Imaging, Three-Dimensional - statistics & numerical data
Interpolation accuracy
Marching Tetrahedra
Models, Chemical
Molecular surface
Small Molecule Libraries - chemistry
Static Electricity
Surface Properties
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Summary:We presented a simple and efficient method to eliminate redundant vertices produced by standard Marching Tetrahedra approach. More than 60% of time cost in quantitative analysis of molecular surface of electrostatic potential can be saved without evident deterioration of accuracy of the results. [Display omitted] ► A new surface refinement method is applied to quantitative molecular surface analysis. ► More than 60% of time cost in surface analysis can be saved by eliminating unreasonably distributed vertices. ► Bisection algorithm improves interpolation accuracy in Marching Tetrahedra significantly. ► Optimal grid spacing for surface analysis was explored. Quantitative analysis of molecular surface is a valuable technique for analyzing non-covalent interaction, studying molecular recognition mode, predicting reactive site and reactivity. An efficient way to realize the analysis was first proposed by Bulat et al. (J. Mol. Model., 16, 1679), in which Marching Tetrahedra (MT) approach commonly used in computer graphics is employed to generate vertices on molecular surface. However, it has been found that the computations of the electrostatic potential in the MT vertices are very expensive and some artificial surface extremes will be presented due to the uneven distribution of MT vertices. In this article, we propose a simple and reliable method to eliminate these unreasonably distributed surface vertices generated in the original MT. This treatment can save more than 60% of total analysis time of electrostatic potential, yet the loss in accuracy is almost negligible. The artificial surface extremes are also largely avoided as a byproduct of this algorithm. In addition, the bisection iteration procedure has been exploited to improve accuracy of linear interpolation in MT. The most appropriate grid spacing for surface analysis has also been investigated. 0.25 and 0.20bohr are recommended to be used for surface analysis of electrostatic potential and average local ionization energy, respectively.
ISSN:1093-3263
1873-4243
DOI:10.1016/j.jmgm.2012.07.004