Large-scale virtual screening on public cloud resources with Apache Spark

Large-scale virtual screening on public cloud resources with Apache Spark

BACKGROUND Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure ra...

Efficient iterative virtual screening with Apache Spark and conformal prediction

BACKGROUND Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out on computer clusters or on large workstations in a brute force manner, by docking and scoring all available ligands. CONTRIBUTION In this study we propose a strategy that is b...

Towards Large Scale Environmental Data Processing with Apache Spark

Currently available environmental datasets are either manually constructed by professionals or automatically generated from the observations provided by sensing devices. Usually, the former are modelled and recorded with traditional general-purpose relational technologies, whereas the latter require more specific scientific array formats and tools. Declarative data processing technologies are a...

Virtual screening on large scale grids

Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated ...

Getting Started with Apache Spark