Efficient unbound docking of rigid molecules

Dina Duhovny; Ruth Nussinov; Haim J. Wolfson

doi:10.1007/3-540-45784-4_14

Efficient unbound docking of rigid molecules

Dina Duhovny^*
, Ruth Nussinov
, Haim J. Wolfson

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

687 Scopus citations

Abstract

We present a new algorithm for unbound (real life) docking of molecules, whether protein–protein or protein-drug. The algorithm carries out rigid docking, with surface variability/flexibility implicitly addressed through liberal intermolecular penetration. The high efficiency of the algorithm is the outcome of several factors: (i) focusing initial molecular surface fitting on localized, curvature based surface patches; (ii) use of Geometric Hashing and Pose Clustering for initial transformation detection; (iii) accurate computation of shape complementarity utilizing the Distance Transform; (iv) efficient steric clash detection and geometric fit scoring based on a multi-resolution shape representation; and (v) utilization of biological information by focusing on hot spot rich surface patches. The algorithm has been implemented and applied to a large number of cases.

Original language	English
Title of host publication	Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings
Editors	Roderic Guigo, Dan Gusfield
Publisher	Springer Verlag
Pages	185-200
Number of pages	16
ISBN (Print)	3540442111, 9783540442110
DOIs	https://doi.org/10.1007/3-540-45784-4_14
State	Published - 2002
Externally published	Yes
Event	2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy Duration: 17 Sep 2002 → 21 Sep 2002

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	2452
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	2nd International Workshop on Algorithms in Bioinformatics, WABI 2002
Country/Territory	Italy
City	Rome
Period	17/09/02 → 21/09/02

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.

Access to Document

10.1007/3-540-45784-4_14

Cite this

Duhovny, D., Nussinov, R., & Wolfson, H. J. (2002). Efficient unbound docking of rigid molecules. In R. Guigo, & D. Gusfield (Eds.), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings (pp. 185-200). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452). Springer Verlag. https://doi.org/10.1007/3-540-45784-4_14

Duhovny, Dina ; Nussinov, Ruth ; Wolfson, Haim J. / Efficient unbound docking of rigid molecules. Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. editor / Roderic Guigo ; Dan Gusfield. Springer Verlag, 2002. pp. 185-200 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Duhovny, D, Nussinov, R & Wolfson, HJ 2002, Efficient unbound docking of rigid molecules. in R Guigo & D Gusfield (eds), Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2452, Springer Verlag, pp. 185-200, 2nd International Workshop on Algorithms in Bioinformatics, WABI 2002, Rome, Italy, 17/09/02. https://doi.org/10.1007/3-540-45784-4_14

Efficient unbound docking of rigid molecules. / Duhovny, Dina; Nussinov, Ruth; Wolfson, Haim J.
Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. ed. / Roderic Guigo; Dan Gusfield. Springer Verlag, 2002. p. 185-200 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2452).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Duhovny D, Nussinov R, Wolfson HJ. Efficient unbound docking of rigid molecules. In Guigo R, Gusfield D, editors, Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Springer Verlag. 2002. p. 185-200. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/3-540-45784-4_14

Efficient unbound docking of rigid molecules

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