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Overview

The molecular docking problem is to determine how molecules interact with other molecules and plays a key role in understanding how cells function. DockingShop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. It provides support to different docking methods rather than a docking method itself. This tool provides molecular graphics interfaces for molecular modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge. Its features include 1) six-degree-of-freedom manipulation of single and multiple molecules 2) refinements of molecular structures by interactive manipulations to explore the actual conformational changes that molecules must undergo to properly bind, 3) determining molecular interactions using visual feedbacks to steer the docking process in real time and 4) modeling and visualizing the details of specific interactions at the atomic level. DockingShop visualizes computational parameters used in scoring functions like free energy, geometric complementarities, inter- and intra-molecular hydrogen bonds, overlaps, and hydrophobic effect as "live" guides to help users navigate a ligand or protein to the potential conformational binding mode, to understand the behavior of a protein structure during the molecular interaction, and to discriminate between native and non-native conformations. Moreover, DockingShop allows users to couple their own scoring functions. Thus, DockingShop permits exploratory and interactive steering of molecular docking by leveraging user knowledge through integrating interactive visualization with real-time simulations.


About the group

PI

  • Silvia N. Crivelli (Scientist, LBNL/QB3)


Postdoctoral Associates

  • James T. Lu (Senior Research Programmer, QB3)
  • Jinhui Ding (Biologist, QB3)