TTP offers an integrated discipline of computational chemistry, bioinformatic system, and data management to support,
- Development of preliminary Structure Activity Relationships (SAR) for hit compounds.
- Identification of structurally similar commercially available analogs via structure-based docking or pharmacophore searching (hit expansion)
- In silicon design
- Virtual screen
Computing Cluster (Ren Lab, 500-core Dell Linux cluster with Gigabit network and a 16 TB disk storage): Virtual screening, drug library design, database searching and data file storage.
GPU Computing Cluster (Ren Lab, 12 GTX1070 GPUs): Molecular dynamics simulations; lead optimization
High performance computing cluster (Lonestar 5, access through TACC, 30048 compute cores, 5 PB disk storage, 40 GPUs): Molecular modeling and molecular dynamics simulations of protein-ligand binding.
Workstations (Tx-Sact, High-end Dell graphics workstation): Visualization and manipulation of molecular systems. Job benchmarking and submission
De novo ligand library design (Daylight Reaction Toolkit): De novo ligand design by linking reactive agents to fragment scaffold.
Ligand based screening (ROCS and EON, OpenEye): Shape and electrostatic similarity based ligand search.
Virtual screening (GOLD (CCDC): Screening of small molecule library against protein targets, predicting binding poses and affinity ranking.
Molecular Modeling (AMBER, GROAMCS, TINKER, OpenMM): Molecular dynamics simulations of protein-ligand binding; advanced binding affinity/free energy calculation for ligand screening and optimization
Visualization (Datawarrior, Pymol, VMD, Chimera): Chemical space visualization and manipulation of protein-ligand systems.