UPDDI Core Facilities and Equipment

Computational Biology and Chemistry

An important aspect of the new vision for drug discovery at the UPDDI is the integration of computational tools in the analysis of drug-target interactions and in developing strategies to advance novel chemical series. The Department of Computational and Systems Biology is well equipped to meet the challenge. Available to the group are over 3100 CPU cores in a 152 node cluster with 9.1 TB memory and 280 TB storage, as well as a cluster of 88 GPUs. In addition, we maintain Windows and Linux servers for sharing files, printers, and other resources. Available modeling software includes CCDC GOLD, MOE, Chimera, VMD, NAMD, and OpenEye Applications and Toolkits: Tripos Sybyl. Research software tools include GNM, ANM, and PCA_NEST servers, ProDy, and several network accessible databases of biological research data are routinely employed. The computation capacity for in silico HTS is up to 16 M compounds per day in a pharmacophore based screen and 2 M compounds in a docking screen when using 184 CPUs.