Graphics processing units (GPUs) have traditionally been used in molecular modeling solely
for visualization of molecular structures and animation of trajectories resulting from …

The biological significance of proteins attracted the scientific community in exploring their
characteristics. The studies shed light on the interaction patterns and functions of proteins in …

Motivation: Modelling protein–protein interactions (PPIs) is an increasingly important aspect
of structural bioinformatics. However, predicting PPIs using in silico docking techniques is …

The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory
data is a common and computationally expensive analysis task. The rate limiting step in the …

Abstract Motivation: The Basic Local Alignment Search Tool (BLAST) is one of the most
widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 53 …

Managing memory between the CPU and GPU is a major challenge in GPU computing. A
programming model, Unified Memory Access (UMA), has been recently introduced by Nvidia …

The application of protein–protein docking in large-scale interactome analysis is a major
challenge in structural bioinformatics and requires huge computing resources. In this work …

Drug screening is an important part of the drug development pipeline for the pharmaceutical
industry. Traditional, lab-based methods are increasingly being augmented with …

Fast Fourier transform (FFT)-based protein ligand docking together with parallel simulated
annealing for both rigid and flexible receptor docking are implemented on graphical …

Irregular applications can be found in different scientific fields. In computer-aided drug
design, molecular docking simulations play an important role in finding promising drug …