Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins: Structure, Function and Bioinformatics. 33(1), 18–29.
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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 structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution structures it is possible to identify these cavities. We have developed a precise algorithm based on alpha shapes for measuring space-filling-based molecular models (such as van der Waals, solvent accessible, and molecular surface descriptions). We applied this method for accurate computation of the surface area and volume of cavities in several proteins. In addition, all of the atoms/residues Lining the cavities are identified, We use this method to study the structure and the stability of proteins, as well as to locate cavities that could contain structural water molecules in the proton transport pathway in the membrane protein bacteriorhodopsin.
Publishing Year
Date Published
1998-10-01
Journal Title
Proteins: Structure, Function and Bioinformatics
Acknowledgement
The software for constructing weighted Delaunay complexes and the alpha shape filters was written by Ernst Mücke and Michael Facello. We thank them forcreating reliable and robust software so that wecan build on their results. The authors thank NSF Meta Center Allocation for providing computational resources. The software VOLBL is part of the standard distribution of the alpha shapes software, andis available at http://alpha.ncsa.uiuc.edu/alpha.
Volume
33
Issue
1
Page
18 - 29
ISSN
IST-REx-ID
Cite this
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins: Structure, Function and Bioinformatics. 1998;33(1):18-29. doi:10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H
Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., & Subramaniam, S. (1998). Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H
Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: II. Inaccessible Cavities in Proteins.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 1998. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H.
J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins,” Proteins: Structure, Function and Bioinformatics, vol. 33, no. 1. Wiley-Blackwell, pp. 18–29, 1998.
Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins: Structure, Function and Bioinformatics. 33(1), 18–29.
Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: II. Inaccessible Cavities in Proteins.” Proteins: Structure, Function and Bioinformatics, vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 18–29, doi:10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H.
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