Speaker: Teeroumanee Nadan,
ACET, University of Reading.
Date/Time: 9th October 2008, 13:00-14:00 (Please note this is on Thursday and not the usual Wednesday slot).
Location: Room G74, Philip Lyle Building.
Map: http://www.info.rdg.ac.uk/maps/maps-display.asp
Abstract:
Protein molecules in living organisms have always interacted with other molecules to achieve a particular function. This happens as one molecule (the ligand) fits into the cavity of a protein molecule (the receptor), a process known as docking. This process is an integral part of drug design and development. The latter can take an average of 12 years; therefore computational tools are used to speed up the docking process. The main problem that scientists face is that these computational tools are desktop-based and it is therefore difficult to see the three-dimensional structure of the ligand and the receptor properly. Hence, they have to rely on docking algorithms to search for receptor-ligand conformation which requires the least interaction energy. Docking algorithms are costly and resource extensive. Thus, it would be preferable for scientists to visualize the 3D structure of a receptor and a ligand and manually dock the ligand into the receptor’s cavity before feeding the new conformations to docking algorithms. If this is achieved, it would enormously decrease docking time as the docking algorithm will not have to carry out a massive conformational search.
To highlight three-dimensional details, a good enough visualization technique should be adopted. This is where Virtual Reality (VR) comes into play. VR is a computer simulation which can project a user into a virtual environment and surround the user for better visualization. This project aims at developing a virtual 3D software for a user-friendly visualization of protein molecules and to make use of users’ interaction with the molecules as a basis for molecular docking in a collaborative environment.
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