title: Haptic-driven, interactive drug design: implementing a GPU-based approach to evaluate the induced fit effect.
abstract: In this paper, we describe a hybrid meta-heuristics method of energy minimization and conformational sampling and its application into our haptic-driven molecular modelling simulator. The proposed method has been designed to suit real-time molecular docking simulations, where the time-lapse between two successive ligand poses is relatively small. In these situations, the energy minimization problem becomes increasingly complex and chaotic. The algorithm is tuned to take advantage of recent advances in GPU computing with asynchronous kernel execution, which has allowed us to include full protein flexibility in the real-time interactive, haptic-driven simulations. Finally, in this paper, we will also discuss the implementation of such high-performance computing approaches in our software, discussing the results of our initial validation studies, highlighting the advantages and limitations of such interactive methodology.
authors.affiliation: School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK. brancalea@cardiff.ac.uk.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Anthopoulos
authors.forename: Gaia
authors.initials: G
authors.lastname: Pasqualetto
authors.forename: Ian
authors.initials: I
authors.lastname: Grimstead
authors.forename: Andrea
authors.initials: A
authors.lastname: Brancale
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D015195:Drug Design; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D012984:Software