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||American English|
|Title of host publication||Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings|
|Editors||Roderic Guigo, Dan Gusfield|
|Number of pages||16|
|ISBN (Print)||3540442111, 9783540442110|
|State||Published - 2002|
|Event||2nd International Workshop on Algorithms in Bioinformatics, WABI 2002 - Rome, Italy|
Duration: 17 Sep 2002 → 21 Sep 2002
|Name||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Conference||2nd International Workshop on Algorithms in Bioinformatics, WABI 2002|
|Period||17/09/02 → 21/09/02|
Bibliographical notePublisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.