Add to ORKGIncludes abstract.Includes bibliographical references (leaves [187]-202).In this work, we describe a Graphics processing unit (GPU) implementation of the Kim-Hummer coarse-grained model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the complex process of migrating the algorithm to a GPU as well as the effect of various GPU approaches and optimisations on algorithm speed-up
Abstract: Modeling the interactions of biological molecules, or docking, is critical to both underst...
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to...
Many essential cell processes, such as the conformation of embedded proteins, membrane permeability,...
Graphics processing unit (GPU) architectures are increasingly used for general purpose computing, pr...
We report a hybrid parallel central and graphics processing units (CPU-GPU) implementation of a coar...
Multiprotein complexes are responsible for many vital cellular functions, and understanding their fo...
Thesis (M.Sc.Eng.) -- Boston UniversityScientists have always felt the desire to perform computation...
The generation of molecular conformations and the evaluation of interaction potentials are common ta...
International audienceThis article outlines the recent developments in the field of large-scale para...
peer reviewedThis article outlines the recent developments in the field of large-scale parallel comp...
Molecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologis...
Background: Protein-DNA docking is a very challenging problem in structural bioinformatics and has i...
Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower compu...
This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynam...
Traditional drug discovery methodology uses a multitude of software packages to design and evaluate ...
Abstract: Modeling the interactions of biological molecules, or docking, is critical to both underst...
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to...
Many essential cell processes, such as the conformation of embedded proteins, membrane permeability,...
Graphics processing unit (GPU) architectures are increasingly used for general purpose computing, pr...
We report a hybrid parallel central and graphics processing units (CPU-GPU) implementation of a coar...
Multiprotein complexes are responsible for many vital cellular functions, and understanding their fo...
Thesis (M.Sc.Eng.) -- Boston UniversityScientists have always felt the desire to perform computation...
The generation of molecular conformations and the evaluation of interaction potentials are common ta...
International audienceThis article outlines the recent developments in the field of large-scale para...
peer reviewedThis article outlines the recent developments in the field of large-scale parallel comp...
Molecular Dynamics (MD) is a simulation technique widely used by computational chemists and biologis...
Background: Protein-DNA docking is a very challenging problem in structural bioinformatics and has i...
Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower compu...
This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynam...
Traditional drug discovery methodology uses a multitude of software packages to design and evaluate ...
Abstract: Modeling the interactions of biological molecules, or docking, is critical to both underst...
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to...
Many essential cell processes, such as the conformation of embedded proteins, membrane permeability,...