TreeDock protein docking software
Summary Predicting protein-protein and protein-ligand docking remains one of the challenging topics of structural biology. The main problems are (i) to reliably estimate the binding free energies of docked states, (ii) to enumerate possible docking orientations at a high resolution, and (iii) to consider mobility of the docking surfaces and structural rearrangements upon interaction. The invention provides a novel algorithm, TreeDock, that addresses the enumeration problem in a rigid-body docking search. By representing molecules as multidimensional binary search trees and by exploring a sufficient number of docking orientations such that two chosen atoms (one from each molecule) are always in contact, TreeDock is able to explore all clash-free orientations, rapidly and at high resolution, to search partial or complete surface areas. The deterministic systematic search of TreeDock is in contrast to other docking programs, most of which use stochastic searches, such as Monte Carlo, or simulated annealing methods.
It has been shown that TreeDock can predict the correct docked conformation for a number of protein-protein and protein-ligand complexes. The program is advantageously used with data from NMR chemical-shift perturbation or residual dipolar coupling studies, or in combination with mutational screening.
Publication: Fahmy and Wagner, 2002, "TreeDock: a tool for protein docking based on minimizing van der Waals energies", J. Am. Chem. Soc. 124(7): 1241-1250.
TreeDock is protected by copyright and is available for field-exclusive or non-exclusive license.
Applications Research tool for structural biology and medicinal chemistry. For Further Information Please Contact the Director of Business Development Alex Szidon Email: email@example.com Telephone: (617) 495-3067
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