Calculation of Force Field Grids for Molecular Docking Using Graphics Processing Unit

Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loo...

Ultra-fast FFT protein docking on graphics processors

MOTIVATION Modelling protein-protein interactions (PPIs) is an increasingly important aspect of structural bioinformatics. However, predicting PPIs using in silico docking techniques is computationally very expensive. Developing very fast protein docking tools will be useful for studying large-scale PPI networks, and could contribute to the rational design of new drugs. RESULTS The Hex spheri...

Using Graphics Processors to Accelerate Protein Docking Calculations

Protein docking is the computationally intensive task of calculating the three-dimensional structure of a protein complex starting from the individual structures of the constituent proteins. In order to make the calculation tractable, most docking algorithms begin by assuming that the structures to be docked are rigid. This article describes some recent developments we have made to adapt our FF...

ACCELERATING MOLECULAR DOCKING and BINDING SITE MAPPING USING FPGAs and GPUs

Cell Charge Approximation for Accelerating Molecular Simulation on CUDA-Enabled GPU

Methods for Molecular Dynamics(MD) simulations are investigated. MD simulation is the widely used computer simulation approach to study the properties of molecular system. Force calculation in MD is computationally intensive. Paral-lel programming techniques can be applied to improve those calculations. The major aim of this paper is to speed up the MD simulation calculations by/using General P...