Chemoinformatics & modeling

TTP offers 1) Assistance in the development of preliminary Structure Activity Relationships (SAR) for hit compounds and the identification of structurally similar commercially available analogs via structure-based docking or pharmacophore searching; 2) Advanced in silico modeling and 3) Early prediction of ADMET properties.

Computing facility:

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

Software capability

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 screeening (GOLD (CCDC), GLIDE (Schrodinger)): 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
Visuailization (Pymol, VMD, Chimera): Visualization and manipulation of protein-ligand systems.