Simulating molecular docking with haptics

Iakovou, Georgios (2015) Simulating molecular docking with haptics. Doctoral thesis, University of East Anglia.

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Abstract

Intermolecular binding underlies various metabolic and regulatory processes of the
cell, and the therapeutic and pharmacological properties of drugs. Molecular docking
systems model and simulate these interactions in silico and allow the study of the
binding process. In molecular docking, haptics enables the user to sense the interaction
forces and intervene cognitively in the docking process. Haptics-assisted docking
systems provide an immersive virtual docking environment where the user can interact
with the molecules, feel the interaction forces using their sense of touch, identify
visually the binding site, and guide the molecules to their binding pose. Despite a
forty-year research e�ort however, the docking community has been slow to adopt this
technology. Proprietary, unreleased software, expensive haptic hardware and limits
on processing power are the main reasons for this. Another signi�cant factor is the
size of the molecules simulated, limited to small molecules.
The focus of the research described in this thesis is the development of an interactive
haptics-assisted docking application that addresses the above issues, and enables
the rigid docking of very large biomolecules and the study of the underlying interactions.
Novel methods for computing the interaction forces of binding on the CPU
and GPU, in real-time, have been developed. The force calculation methods proposed
here overcome several computational limitations of previous approaches, such as precomputed
force grids, and could potentially be used to model molecular
exibility
at haptic refresh rates. Methods for force scaling, multipoint collision response, and
haptic navigation are also reported that address newfound issues, particular to the
interactive docking of large systems, e.g. force stability at molecular collision. The
i
ii
result is a haptics-assisted docking application, Haptimol RD, that runs on relatively
inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary
hardware).

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Computing Sciences
Depositing User:	Users 2259 not found.
Date Deposited:	22 Jun 2016 14:17
Last Modified:	22 Jun 2016 14:17
URI:	https://ueaeprints.uea.ac.uk/id/eprint/59468
DOI:

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