DOI: 10.1002/prot.340160306. Surface motifs by a computer vision technique: Searches, detection, and implications for protein

Surface motifs by a computer vision technique: Searches, detection, and implications for protein–ligand recognition

10.1002/prot.340160306

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractWe describe the application of a method geared toward structural and surface comparison of proteins. The method is based on the Geometric Hashing Paradigm adapted from Computer Vision. It allows for comparison of any two sets of 3‐D coordinates, such as protein backbones, protein core or protein surface motifs, and small molecules such as drugs. Here we apply our method to 4 types of comparisons between pairs of molecules: (1) comparison of the backbones of two protein domains; (2) search for a predefined 3‐D Cαmotif within the full backbone of a domain; and in particular, (3) comparison of the surfaces of two receptor proteins; and (4) comparison of the surface of a receptor to the surface of a ligand. These aspects complement each other and can contribute toward a better understandingof protein structure and biomolecular recognition. Searches for 3‐D surface motifs can be carried out on either receptors or on ligands. The latter may result in the detection of pharmacophoric patterns. If the surfaces of the binding sites of either the receptors or of the ligands are relatively similar, surface superpositioning may aid significantly in the docking problem. Currently, only distance invariants are used in the matching, although additional geometric surface invariants are considered. The speed of our Geometric Hashing algorithm is encouraging, with a typical surface comparison taking only seconds or minutes of CPU time on a SUN 4 SPARC workstation. The direct application of this method to the docking problem is also discussed. We demonstrate the success of this methodin its application to two members of the globin family and to two dehydrogenases. © 1993 Wiley‐Liss, Inc.

Bibliography

Fischer, D., Norel, R., Wolfson, H., & Nussinov, R. (1993). Surface motifs by a computer vision technique: Searches, detection, and implications for proteinâligand recognition. Proteins: Structure, Function, and Bioinformatics, 16(3), 278â292. Portico.

Authors 4

Daniel Fischer (first)
Raquel Norel (additional)
Haim Wolfson (additional)
Ruth Nussinov (additional)

References 29 Referenced 57

Dates

Type	When
Created	20 years, 3 months ago (May 28, 2005, 9:28 p.m.)
Deposited	8 months ago (Jan. 1, 2025, 7:58 a.m.)
Indexed	2 months ago (July 7, 2025, 8:04 a.m.)
Issued	32 years, 2 months ago (July 1, 1993)
Published	32 years, 2 months ago (July 1, 1993)
Published Online	21 years, 7 months ago (Feb. 3, 2004)
Published Print	32 years, 2 months ago (July 1, 1993)

Funders 0

None

BibTeX

@article{Fischer_1993, title={Surface motifs by a computer vision technique: Searches, detection, and implications for protein–ligand recognition}, volume={16}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.340160306}, DOI={10.1002/prot.340160306}, number={3}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Fischer, Daniel and Norel, Raquel and Wolfson, Haim and Nussinov, Ruth}, year={1993}, month=jul, pages={278–292} }

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