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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.
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