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 10⁸ 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).