DOI: 10.1002/jmr.300080603. Occluded molecular surface: Analysis of protein packing

Occluded molecular surface: Analysis of protein packing

10.1002/jmr.300080603

Crossref journal-article

Wiley

Journal of Molecular Recognition (311)

Abstract

AbstractWe describe a novel method to calculate the packing interactions in protein structural models. The method calculates the interatomic occluded surface areas for each atom in the protein model. The identification of, and degree of interaction with, neighboring atoms is accomplished by extending surface normal from a dot surface of each atom to the point of intersection with neighboring atoms. The combined occluded and non‐occluded surface areas may be normalized for the amino acid composition of the protein providing a single parameter, the normalized protein surface ratio, which is diagnostic for native‐like Structures. Individual residues in the model which are in infrequent occluded surface environments may be identified. The method provides a means to explicitly describe packing densities and packing environments of individual atoms in a protein model. Finally, the method allows estimation of the complementarity between any interacting molecules, for example a ligand binding to a receptor.

Bibliography

Pattabiraman, N., Ward, K. B., & Fleming, P. J. (1995). Occluded molecular surface: Analysis of protein packing. Journal of Molecular Recognition, 8(6), 334â344. Portico.

Authors 3

N. Pattabiraman (first)
K. B. Ward (additional)
P. J. Fleming (additional)

References 38 Referenced 106

{'key': 'e_1_2_1_2_1', 'first-page': '107', 'volume-title': 'Crystallographic Databases–Information Content, Software Systems, Scientific Applications', 'author': 'Abola E. E.', 'year': '1987'} / Crystallographic Databases–Information Content, Software Systems, Scientific Applications by Abola E. E. (1987)
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Dates

Type	When
Created	20 years, 3 months ago (May 29, 2005, 6:38 a.m.)
Deposited	1 year, 10 months ago (Oct. 25, 2023, 10:50 p.m.)
Indexed	2 months, 1 week ago (June 26, 2025, 9:10 a.m.)
Issued	29 years, 10 months ago (Nov. 1, 1995)
Published	29 years, 10 months ago (Nov. 1, 1995)
Published Online	21 years, 7 months ago (Feb. 3, 2004)
Published Print	29 years, 10 months ago (Nov. 1, 1995)

Funders 0

None

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