DOI: 10.1002/pro.5560020318. Mapping the surface properties of macromolecules

Mapping the surface properties of macromolecules

10.1002/pro.5560020318

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractMethods are presented for the rapid computation of schematic projections of the surfaces of macromolecules, similar to the “roadmaps” used to illustrate the surfaces of viruses (Rossmann, M.G. & Palmenberg, A.C., 1988, Virology 164, 373–382). Several types of projections are described, extending the application of “roadmaps” to the external surfaces of all macromolecules and their interior binding pockets and pores. The surface projections, showing the positions of residues, can be colored, shaded, contoured, and annotated to show physical, sequence, or functional properties such as surface topology, hydrophobicity, or sequence conservation, for example. The automated procedures are useful for surveys of the surface features of proteins sharing similar functional properties.

Bibliography

Chapman, M. S. (1993). Mapping the surface properties of macromolecules. Protein Science, 2(3), 459â469. Portico.

Authors 1

Michael S. Chapman (first)

References 27 Referenced 35

{'key': 'e_1_2_1_2_2', 'volume-title': 'PostScript Language Reference Manual', 'author': 'Adobe Systems, Inc.', 'year': '1990'} / PostScript Language Reference Manual by Adobe Systems, Inc. (1990)
10.1038/206757a0
Chapman M.S.&Rossmann M.G.(1993). Structure sequence and function correlations among parvoviruses.Virology in press. (10.1006/viro.1993.1288)
10.1126/science.6879170
{'key': 'e_1_2_1_6_2', 'first-page': '353', 'volume-title': 'Atlas of Protein Sequence and Structure', 'author': 'Dayhoff M.O.', 'year': '1979'} / Atlas of Protein Sequence and Structure by Dayhoff M.O. (1979)
10.1016/0022-2836(74)90598-1
10.1038/319199a0
{'key': 'e_1_2_1_9_2', 'first-page': '369', 'article-title': 'Hydrophobic parameters π of amino‐acid side chains from the partitioning of N‐acetyl‐amino‐acid amides', 'volume': '18', 'author': 'Fauchere J.‐L.', 'year': '1983', 'journal-title': 'Eur. J. Med. Chem. Chim. Ther.'} / Eur. J. Med. Chem. Chim. Ther. / Hydrophobic parameters π of amino‐acid side chains from the partitioning of N‐acetyl‐amino‐acid amides by Fauchere J.‐L. (1983)
10.1093/nar/14.16.6745
{'key': 'e_1_2_1_11_2', 'first-page': '665', 'volume-title': 'The Enzymes', 'author': 'Imoto T.', 'year': '1972'} / The Enzymes by Imoto T. (1972)
10.1107/S0021889878013308
10.1107/S0108767390010224
10.1038/282875a0
Kim K.H. Willingmann P. Gong Z.X. Kremer M.J. Chapman M.S. Minor I. Oliveira M.A. Rossmann M.G. Andries K. Diana G.D. Dutko F.J. McKinlay M.A. &Pevear D.C.(1993). A comparison of the anti‐rhinoviral drug binding pocket in HRV14 and HRV1A.J. Mol. Biol. in press. (10.2210/pdb2hwb/pdb)
10.1016/0022-2836(89)90293-3
10.1107/S0021889891004399
10.1038/355137a0
10.1093/jac/16.3.284
10.1073/pnas.90.2.507
{'key': 'e_1_2_1_21_2', 'first-page': '211', 'volume-title': 'Molecular Aspects of Picornavirus Infection and Detection. Semler', 'author': 'Palmenberg A.C.', 'year': '1989'} / Molecular Aspects of Picornavirus Infection and Detection. Semler by Palmenberg A.C. (1989)
10.1128/jvi.63.5.2002-2007.1989
10.1038/317145a0
10.1016/0042-6822(88)90550-8
10.1128/JVI.57.1.246-257.1986
10.1126/science.3018924
10.1016/S0021-9258(20)65098-0
10.1126/science.2006420

Dates

Type	When
Created	15 years, 1 month ago (July 12, 2010, 1:43 a.m.)
Deposited	1 year, 10 months ago (Oct. 25, 2023, 9:57 p.m.)
Indexed	5 months, 2 weeks ago (March 19, 2025, 8:55 a.m.)
Issued	32 years, 6 months ago (March 1, 1993)
Published	32 years, 6 months ago (March 1, 1993)
Published Online	16 years, 8 months ago (Dec. 31, 2008)
Published Print	32 years, 6 months ago (March 1, 1993)

Funders 2

National Science Foundation
National Institutes of Health, and Medical Research Council

BibTeX

@article{Chapman_1993, title={Mapping the surface properties of macromolecules}, volume={2}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560020318}, DOI={10.1002/pro.5560020318}, number={3}, journal={Protein Science}, publisher={Wiley}, author={Chapman, Michael S.}, year={1993}, month=mar, pages={459–469} }

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