In silico drug discovery approaches on grid computing infrastructures.
The first step in finding a "drug" is screening chemical compound databases against a protein target. In silico approaches like virtual screening by molecular docking are well established in modern drug discovery. As molecular databases of compounds and target structures are becoming larger and more and more computational screening approaches are available, there is an increased need in compute power and more complex workflows. In this regard, computational Grids are predestined and offer seamless compute and storage capacity. In recent projects related to pharmaceutical research, the high computational and data storage demands of large-scale in silico drug discovery approaches have been addressed by using Grid computing infrastructures, in both; pharmaceutical industry as well as academic research. Grid infrastructures are part of the so-called eScience paradigm, where a digital infrastructure supports collaborative processes by providing relevant resources and tools for data- and compute-intensive applications. Substantial computing resources, large data collections and services for data analysis are shared on the Grid infrastructure and can be mobilized on demand. This review gives an overview on the use of Grid computing for in silico drug discovery and tries to provide a vision of future development of more complex and integrated workflows on Grids, spanning from target identification and target validation via protein-structure and ligand dependent screenings to advanced mining of large scale in silico experiments.
Wolf
Antje
A
Department of Bioinformatics, Fraunhofer-Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. antje.wolf@scai.fraunhofer.dee
Shahid
Mohammad
M
Kasam
Vinod
V
Ziegler
Wolfgang
W
Hofmann-Apitius
Martin
M
D003198:Computer Simulation; D017076:Computer-Aided Design; D016503:Drug Delivery Systems; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D004345:Drug Industry / Q000379:methods; D006801:Humans; D008024:Ligands; D011506:Proteins / Q000378:metabolism
D008024:Ligands; D011506:Proteins