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DockIT: Interactive Flexible Molecular Docking
Participants
Dr. Georgios Iakovou
Summary
Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to structure-based drug design (SBDD) and educating students about biomolecular interactions. For SBDD, it enables expertise and intuition to be brought to bear in the drug design process. In education, it can teach students about the most basic level of biomolecular function. This project has resulted in DockIT, software for interactive molecular docking. Using the method of linear response on explicit solvent molecular dynamics simulations, DockIT can model both global and local conformational changes within the receptor due to forces of interaction with the ligand. It has real-time flexible molecular surface rendering and can show the real-time formation and breaking of hydrogen bonds, both between the ligand and receptor and within the receptor itself as it smoothly changes conformation. We are currently exploring additional methods to model protein flexibility and methods to enhance the real-time performance of the molecular graphics.
DockIT is available for download.
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Publications
[1]Iakovou, G., Laycock, S.D. and Hayward, S., "Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT" , Journal of Chemical Information and Modeling, 2022
[2 ]Matthews, N., Kitao, A., Laycock, S.D. and Hayward, S., "Haptic-assisted interactive molecular docking incorporating receptor flexibility" , Journal of Chemical Information and Modeling, 2019
[3] Iakovou, G., Hayward, S. and Laycock, S.D., "Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics", Journal of Chemical Information and Modeling, 2017