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Analytical molecular surface calculation
Abstract
A computer algorithm is presented for calculating the part of the van der Waals surface of molecule that is accessible to solvent. The solvent molecule is modeled by a sphere. This sphere is, in effect, rolled over the molecule to generate a smooth outer-surface contour. This surface contour is made up of pieces of spheres and tori that join at circular arcs. The spheres, tori and arcs are defined by analytical expressions in terms of the atomic coordinates, van der Waals radii and the probe radius. The area of each surface piece may be calculated analytically and the surface may be displayed on either vector or raster computer-graphics systems. These methods are useful for studying the structure and interactions of proteins and nucleic acids.
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Cited by
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0897 · Cited by 6,763
PatchDock and SymmDock: servers for rigid and symmetric docking
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
Liang, J., Woodward, C., & Edelsbrunner, H. (1998) · Protein Science · doi:10.1002/pro.5560070905 · Cited by 1,057
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9
McLellan, J. S., Pancera, M., Carrico, C., Gorman, J., Julien, J.-P., Khayat, R., Louder, R., Pejchal, R., Sastry, M., Dai, K., et al. (2011) · Nature · doi:10.1038/nature10696 · Cited by 830
Metadata
- Authors
- Connolly, M. L.
- Venue
- Journal of Applied Crystallography
- Published
- 1983-10-01
- Volume
- 16
- Issue
- 5
- Pages
- 548-558
- ISSN
- 0021-8898 (ISSN-L)
- OpenAlex
- W2063831812
- Cited by
- 2,508
- References
- 0
- FWCI
- 4.14
- Type
- journal article
- Language
- en
- Open access
- closed
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- Connolly, M. L. (1983). Analytical molecular surface calculation. Journal of Applied Crystallography. https://doi.org/10.1107/s0021889883010985
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
