Advertisement
No access
Article

Solvent-Accessible Surfaces of Proteins and Nucleic Acids

Science
19 Aug 1983
Vol 221, Issue 4612
pp. 709-713

Abstract

A method is presented for analytically calculating a smooth, three-dimensional contour about a molecule. The molecular surface envelope may be drawn on either color raster computer displays or real-time vector computer graphics systems. Molecular areas and volumes may be computed analytically from this surface representation. Unlike most previous computer graphics representations of molecules, which imitate wire models or space-filling plastic spheres, this surface shows only the atoms that are accessible to solvent. This analytical method extends the earlier dot surface numerical algorithm, which has been applied in enzymology, rational drug design, immunology, and understanding DNA base sequence recognition.

Get full access to this article

View all available purchase options and get full access to this article.

References

ALDEN, C.J., SOLVENT-ACCESSIBLE SURFACES OF NUCLEIC-ACIDS, JOURNAL OF MOLECULAR BIOLOGY 132: 411 (1979).
Barry, C. D., Computers in Life Science Research: 137 (1975).
Barry, C. D., Computer Systems Laboratory, Washington University, Technical Memo 229 (1976).
BERNSTEIN, F.C., PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES, JOURNAL OF MOLECULAR BIOLOGY 112: 535 (1977).
BLANEY, J.M., COMPUTER-GRAPHICS IN DRUG DESIGN - MOLECULAR MODELING OF THYROID-HORMONE PRE-ALBUMIN INTERACTIONS, JOURNAL OF MEDICINAL CHEMISTRY 25: 785 (1982).
BLINN, J.F., ACM T GRAPHIC 1: 235 (1982).
Brooks, F. P., Proceedings of the 1977 International Federation of Information Processing: 625 (1977).
Connolly, M. L., Journal of Applied Crystallography 16: 548 (1983).
CONNOLLY, M.L., QCPE BULLETIN 1: 75 (1981).
CONNOLLY, M.L., THESIS U CALIFORNIA (1981).
CONNOLLY, M.L., unpublished data.
Diamond, R., Computational Crystallography: 318 (1982).
Dickerson, R. E., Hemoglobin: Structure, Function, Evolution, and Pathology: 136 (1983).
do Carmo, M. P., Differential Geometry of Curves and Surfaces: 274 (1976).
Drew, H., Proceedings of the National Academy of Sciences of the United States of America 79: 4040 (1982).
Drew, H., Proceedings of the National Academy of Sciences of the United States of America 78: 2179 (1981).
FELDMANN, R.J., INTERACTIVE COMPUTER SURFACE GRAPHICS APPROACH TO STUDY OF ACTIVE-SITE OF BOVINE TRYPSIN, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 75: 5409 (1978).
Foley, J. D., Fundamentals of Interactive Computer Graphics (1982).
FOX, R.O., A VOLTAGE-GATED ION CHANNEL MODEL INFERRED FROM THE CRYSTAL-STRUCTURE OF ALAMETHICIN AT 1.5-A RESOLUTION, NATURE 300: 325 (1982).
GETZOFF, E.D., THESIS DUKE U DURHAM (1982).
GOLDSMITH, E, STRUCTURE OF MALTOHEPTAOSE BY DIFFERENCE FOURIER METHODS AND A MODEL FOR GLYCOGEN, JOURNAL OF MOLECULAR BIOLOGY 156: 411 (1982).
GREER, J, MACROMOLECULAR SHAPE AND SURFACE MAPS BY SOLVENT EXCLUSION, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 75: 303 (1978).
HANSCH, C, COMPARISON OF THE INHIBITION OF ESCHERICHIA-COLI AND LACTOBACILLUS-CASEI DIHYDROFOLATE-REDUCTASE BY 2,4-DIAMINO-5-(SUBSTITUTED-BENZYL)PYRIMIDINES - QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS, X-RAY CRYSTALLOGRAPHY, AND COMPUTER-GRAPHICS IN STRUCTURE ACTIVITY ANALYSIS, JOURNAL OF MEDICINAL CHEMISTRY 25: 777 (1982).
HUBER, R, STRUCTURE OF COMPLEX FORMED BY BOVINE TRYPSIN AND BOVINE PANCREATIC TRYPSIN-INHIBITOR .2. CRYSTALLOGRAPHIC REFINEMENT AT 1.9 A RESOLUTION, JOURNAL OF MOLECULAR BIOLOGY 89: 73 (1974).
Johnson, C. K., Oak Ridge National Laboratory Technical Report 5138 (1976).
Jones, T. A., Computational Crystallography: 303 (1982).
KNOWLTON, K, ATOMS-A 3-D OPAQUE MOLECULE SYSTEM FOR COLOR PICTURES OF SPACE-FILLING OR BALL-AND-STICK MODELS, COMPUTERS & CHEMISTRY 1: 161 (1977).
KUNTZ, I.D., A GEOMETRIC APPROACH TO MACROMOLECULE-LIGAND INTERACTIONS, JOURNAL OF MOLECULAR BIOLOGY 161: 269 (1982).
LANGRIDGE, R, REAL-TIME COLOR GRAPHICS IN STUDIES OF MOLECULAR-INTERACTIONS, SCIENCE 211: 661 (1981).
LEE, B, INTERPRETATION OF PROTEIN STRUCTURES - ESTIMATION OF STATIC ACCESSIBILITY, JOURNAL OF MOLECULAR BIOLOGY 55: 379 (1971).
LERNER, R.A., TAPPING THE IMMUNOLOGICAL REPERTOIRE TO PRODUCE ANTIBODIES OF PREDETERMINED SPECIFICITY, NATURE 299: 592 (1982).
MAX, N.L., COMPUT GRAPH 13: 165 (1979).
MONACO, H.L., 3-DIMENSIONAL STRUCTURES OF ASPARTATE CARBAMOYLTRANSFERASE FROM ESCHERICHIA-COLI AND OF ITS COMPLEX WITH CYTIDINE TRIPHOSPHATE, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 75: 5276 (1978).
Newman, W. N., Principles of Interactive Computer Graphics: 367 (1979).
O'DONNELL, T.J., COMPUTER GRAPHICS 15: 133 (1981).
Olson, A. J., Antibody Structure (n.d.).
Olson, A. J., Virus Wars, computer-generated film presented at the International School of Crystallography, Conference on Crystallography in Molecular Biology, Italy, June (1982).
PORTER, T.K., COMP GRAPHICS 13: 234 (1979).
PORTER, T.K., COMP GRAPHICS 12: 282 (1978).
RICHARDS, F.M., AREAS, VOLUMES, PACKING, AND PROTEIN-STRUCTURE, ANNUAL REVIEW OF BIOPHYSICS AND BIOENGINEERING 6: 151 (1977).
RICHARDS, F.M., INTERPRETATION OF PROTEIN STRUCTURES - TOTAL VOLUME, GROUP VOLUME DISTRIBUTIONS AND PACKING DENSITY, JOURNAL OF MOLECULAR BIOLOGY 82: 1 (1974).
RICHMOND, T.J., PACKING OF ALPHA-HELICES - GEOMETRICAL CONSTRAINTS AND CONTACT AREAS, JOURNAL OF MOLECULAR BIOLOGY 119: 537 (1978).
SHRAKE, A, ENVIRONMENT AND EXPOSURE TO SOLVENT OF PROTEIN ATOMS - LYSOZYME AND INSULIN, JOURNAL OF MOLECULAR BIOLOGY 79: 351 (1973).
SMITH, R.N., THE USE OF CRYSTALLOGRAPHY, GRAPHICS, AND QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS IN THE ANALYSIS OF THE PAPAIN HYDROLYSIS OF X-PHENYL HIPPURATES, ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS 215: 319 (1982).
SPRANG, S, ANALYSIS OF AN ALLOSTERIC BINDING-SITE - THE NUCLEOSIDE INHIBITOR SITE OF PHOSPHORYLASE-A, BIOCHEMISTRY 21: 2036 (1982).
SPRANG, S.R., CATALYTIC SITE OF GLYCOGEN-PHOSPHORYLASE - STRUCTURE OF THE T-STATE AND SPECIFICITY FOR ALPHA-D-GLUCOSE, BIOCHEMISTRY 21: 5364 (1982).
SUSSMAN, J.L., CRYSTAL-STRUCTURE OF YEAST PHENYLALANINE TRANSFER-RNA .1. CRYSTALLOGRAPHIC REFINEMENT, JOURNAL OF MOLECULAR BIOLOGY 123: 607 (1978).
TAINER, J.A., DETERMINATION AND ANALYSIS OF THE 2A STRUCTURE OF COPPER, ZINC SUPEROXIDE-DISMUTASE, JOURNAL OF MOLECULAR BIOLOGY 160: 181 (1982).
Weiner, P. K., Proceedings of the National Academy of Sciences of the United States of America 79: 3754 (1982).
WHITTED, T, AN IMPROVED ILLUMINATION MODEL FOR SHADED DISPLAY, COMMUNICATIONS OF THE ACM 23: 343 (1980).
WHITTED, T, SOME RECENT ADVANCES COMPUTER-GRAPHICS, SCIENCE 215: 767 (1982).

(0)eLetters

eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.

Log In to Submit a Response

No eLetters have been published for this article yet.

Information & Authors

Information

Published In

Science
Volume 221 | Issue 4612
19 August 1983

Submission history

Published in print: 19 August 1983

Permissions

Request permissions for this article.

Authors

Affiliations

Michael L. Connolly
Molecular Biology Department. Research Institute of Scripps Clinic, La Jolla, California 92037.

Metrics & Citations

Metrics

Article Usage

Altmetrics

Citations

Cite as

Export citation

Select the format you want to export the citation of this publication.

Cited by

  1. Fluorescent Guest Molecules Report Ordered Inner Phase of Host Capsules in Solution, Science, 309, 5743, (2037-2039), (2021)./doi/10.1126/science.1116579
    Abstract
  2. Automated structure discovery in atomic force microscopy, Science Advances, 6, 9, (2020)./doi/10.1126/sciadv.aay6913
    Abstract
  3. The Crystal Structure of Urease from Klebsiella aerogenes, Science, 268, 5213, (998-1004), (1995)./doi/10.1126/science.7754395
    Abstract
  4. Structure-Based Discovery of Inhibitors of Thymidylate Synthase, Science, 259, 5100, (1445-1450), (1993)./doi/10.1126/science.8451640
    Abstract
  5. The Crystal Structure of Lysin, a Fertilization Protein, Science, 262, 5141, (1864-1867), (1993)./doi/10.1126/science.8266073
    Abstract
  6. Human CksHs2 Atomic Structure: a Role for Its Hexameric Assembly in Cell Cycle Control, Science, 262, 5132, (387-395), (1993)./doi/10.1126/science.8211159
    Abstract
  7. Structure-Based Strategies for Drug Design and Discovery, Science, 257, 5073, (1078-1082), (1992)./doi/10.1126/science.257.5073.1078
    Abstract
  8. Response of a Protein Structure to Cavity-Creating Mutations and Its Relation to the Hydrophobic Effect, Science, 255, 5041, (178-183), (1992)./doi/10.1126/science.1553543
    Abstract
  9. Three-Dimensional Solution Structure of Plastocyanin from the Green Alga Scenedesmus obliquus, Science, 240, 4850, (314-317), (1988)./doi/10.1126/science.3353725
    Abstract
  10. Synthetic Amphiphilic Peptide Models for Protein Ion Channels, Science, 240, 4856, (1177-1181), (1988)./doi/10.1126/science.2453923
    Abstract
  11. See more
Loading...

View Options

Check Access

Log in to view the full text

AAAS ID LOGIN

AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.

Log in via OpenAthens.
Log in via Shibboleth.

More options

Purchase digital access to this article

Download and print this article for your personal scholarly, research, and educational use.

Purchase this issue in print

Buy a single issue of Science for just $15 USD.

View options

PDF format

Download this article as a PDF file

Download PDF

Media

Figures

Multimedia

Tables

Share

Share

Share article link

Share on social media