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 proceedingConference contributionpeer-review

635 Scopus citations


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 languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings
EditorsRoderic Guigo, Dan Gusfield
PublisherSpringer Verlag
Number of pages16
ISBN (Print)3540442111, 9783540442110
StatePublished - 2002
Event2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy
Duration: 17 Sep 200221 Sep 2002

Publication series

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


Conference2nd International Workshop on Algorithms in Bioinformatics, WABI 2002


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