Efficient iterative virtual screening with Apache Spark and conformal prediction

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...

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...

Getting Started with Apache Spark

Balanced Graph Partitioning with Apache Spark

A significant part of the data produced every day by online services is structured as a graph. Therefore, there is the need for efficient processing and analysis solutions for large scale graphs. Among the others, the balanced graph partitioning is a well known NP-complete problem with a wide range of applications. Several solutions have been proposed so far, however most of the existing state-...

SPARQL query processing with Apache Spark

The number and the size of linked open data graphs keep growing at a fast pace and confronts semantic RDF services with problems characterized as Big data. Distributed query processing is one of them and needs to be efficiently addressed with execution guaranteeing scalability, high availability and fault tolerance. RDF data management systems requiring these properties are rarely built from sc...