A number of current trends that are being adopted to reshape the field of high-performance computing exist, including multi-core systems, accelerators, and software frameworks for large-scale intrinsically parallel applications. These trends intersect with recent developments in computational chemistry to provide new capabilities for computer-aided drug discovery. Although this review focuses primarily on the application domains of molecular modeling and biomolecular simulation, these computing changes are relevant for other computationally intensive tasks, such as instrument data processing and chemoinformatics.

High throughput docking (HTD) using high performance computing platforms is a multidisciplinary challenge. To handle HTD data effectively and efficiently, we have developed a distributed virtual screening data management system (DVSDMS) in which the data handling and the distribution of jobs are realized by the open-source structured query language database software MySQL. The essential concept of DVSDMS is the separation of the data management from the docking and ranking applications. DVSDMS can be used to dock millions of molecules effectively, monitor the process in real time, analyze docking results promptly, and process up to 10(8) poses by energy ranking techniques. In an HTD campaign to identify kinase inhibitors a low cost Linux PC has allowed DVSDMS to efficiently assign the workload to more than 500 computing clients. Notably, in a stress test of DVSDMS that emulated a large number of clients, about 60 molecules per second were distributed to the clients for docking, which indicates that DVSDMS can run efficiently on very large compute cluster (up to about 40000 cores).