Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function and Bioinformatics. 33(1), 1–17.
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Journal Article
| Published
| English
Scopus indexed
Author
Liang, Jie;
Edelsbrunner, HerbertISTA 
;
Fu, Ping;
Sudhakar, Pamidighantam;
Subramaniam, Shankar
;
Fu, Ping;
Sudhakar, Pamidighantam;
Subramaniam, ShankarAbstract
The size and shape of macromolecules such as proteins and nucleic acids play an important role in their functions. Prior efforts to quantify these properties have been based on various discretization or tessellation procedures involving analytical or numerical computations. In this article, we present an analytically exact method for computing the metric properties of macromolecules based on the alpha shape theory. This method uses the duality between alpha complex and the weighted Voronoi decomposition of a molecule. We describe the intuitive ideas and concepts behind the alpha shape theory and the algorithm for computing areas and volumes of macromolecules. We apply our method to compute areas and volumes of a number of protein systems. We also discuss several difficulties commonly encountered in molecular shape computations and outline methods to overcome these problems. (C) 1998 Wiley-Liss, Inc.
Publishing Year
Date Published
1998-10-01
Journal Title
Proteins: Structure, Function and Bioinformatics
Publisher
Wiley-Blackwell
Acknowledgement
We thank Michael Facello for the torus area formula and suggestion regarding computation of MS model from SA model. We thank Nataraj Akkiraju, Patrick Moran, and Marcus Wagner for interesting discussionson the topic of this article and for help in the generationof two- and three-dimensional illustrations. We thank NSF Meta Center Allocation for providing computational resources. The software VOLBL is available at:http://alpha.ncsa.uiuc.edu/alpha.
Volume
33
Issue
1
Page
1 - 17
ISSN
IST-REx-ID
Cite this
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function and Bioinformatics. 1998;33(1):1-17. doi:10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O
Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., & Subramaniam, S. (1998). Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O
Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 1998. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O.
J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape,” Proteins: Structure, Function and Bioinformatics, vol. 33, no. 1. Wiley-Blackwell, pp. 1–17, 1998.
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function and Bioinformatics. 33(1), 1–17.
Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: I. Molecular Area and Volume through Alpha Shape.” Proteins: Structure, Function and Bioinformatics, vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 1–17, doi:10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O.
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