Efficient molecular surface generation using level-set methods

Journal of Molecular Graphics & Modelling
Tolga CanYuan-Fang Wang

Abstract

Molecules interact through their surface residues. Calculation of the molecular surface of a protein structure is thus an important step for a detailed functional analysis. One of the main considerations in comparing existing methods for molecular surface computations is their speed. Most of the methods that produce satisfying results for small molecules fail to do so for large complexes. In this article, we present a level-set-based approach to compute and visualize a molecular surface at a desired resolution. The emerging level-set methods have been used for computing evolving boundaries in several application areas from fluid mechanics to computer vision. Our method provides a uniform framework for computing solvent-accessible, solvent-excluded surfaces and interior cavities. The computation is carried out very efficiently even for very large molecular complexes with tens of thousands of atoms. We compared our method to some of the most widely used molecular visualization tools (Swiss-PDBViewer, PyMol, and Chimera) and our results show that we can calculate and display a molecular surface 1.5-3.14 times faster on average than all three of the compared programs. Furthermore, we demonstrate that our method is able to detect al...Continue Reading

References

Jan 1, 1977·Annual Review of Biophysics and Bioengineering·F M Richards
Sep 1, 1995·Trends in Biochemical Sciences·R A Sayle, E J Milner-White
Dec 1, 1994·Protein Science : a Publication of the Protein Society·S J Hubbard, P Argos
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 21, 2003·Protein Engineering·Kazufumi TakanoKatsuhide Yutani
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin

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Citations

Oct 9, 2007·Bioinformatics·Min HuQunsheng Peng
Apr 24, 2010·International Journal of Biomedical Imaging·Joachim Giard, Benoît Macq
Mar 22, 2013·PloS One·Dan V NicolauDan V Nicolau
Apr 4, 2014·BMC Bioinformatics·Hsin-Wei WangTun-Wen Pai
Nov 3, 2012·Journal of Molecular Graphics & Modelling·Minxin ChenBenzhuo Lu
Oct 6, 2009·Computer Methods in Applied Mechanics and Engineering·Chandrajit L BajajQin Zhang
Apr 22, 2008·Journal of Molecular Graphics & Modelling·Derek Juba, Amitabh Varshney
Jun 24, 2008·Journal of Molecular Graphics & Modelling·Matthieu ChaventBernard Maigret
Jan 1, 2013·Computational and Structural Biotechnology Journal·Jie LiPatrice Koehl
Nov 28, 2012·Journal of Chemical Theory and Computation·Jun WangRay Luo
Sep 4, 2007·The Journal of Chemical Physics·Li-Tien ChengBo Li
Sep 5, 2018·Visual Computing for Industry, Biomedicine and Art·Sheng GuiBen-Zhuo Lu
Feb 13, 2010·Journal of Chemical Theory and Computation·Li-Tien ChengBo Li
May 28, 2021·Journal of Computational Chemistry·Leighton Wilson, Robert Krasny
Jan 11, 2011·Journal of Chemical Theory and Computation·Minxin Chen, Benzhuo Lu
Nov 20, 2015·Journal of Chemical Theory and Computation·I SakalliE W Knapp

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