[Works]1. Mainly focused on Targeted Protein Degraders for Non-CRBN ligase systems.- Discovery of active compounds as the protein-protein binding enhancer by conventional in silico screening methods.- Rigorous refinement of E3-POI binding complex (PPI) by molecular dynamics simulations.- Determination of induced-fit binding poses of hit (active) compounds in the target E3-POI complex structures using MD simulation and flexible docking.- SAR strategy collaborating with medicinal chemists2. Development GNN-based deep learning models.- Model for discriminating kinase hinge binding motifs in chemical structures.- Novel loss function to improve noticeably the discriminating powers3. Utilization and development of essential computational chemist methodologies.- Thermodynamic integration method (or FEP) in the Amber MD engine to optimize hit/lead chemicals.- Combination of FEP as the oracle in Active Learning procedure to accelerate hit/lead optimization.- Development of hybrid AA/CG force field.- Multi-scale MD simulations for large-scale E3 ligase complex systems.- Fragment Molecular Orbital (FMO) as the pair-interaction analyzer for protein-ligand complexes using GAMESS

Structure-based drug discovery (HDAC, Kinase (ALK), KRas)Analysis of dynamics or allostery of protein-ligand complex (KRas)Analysis of FMO(QM method in GAMESS)-based protein-ligand interactionDevelopment of prediction models of chemical properties using deep learning methods (pytorch, tensorflow)Development of novel algorithms of molecular modelings (docking, scaffold hopping, molecular descriptors) - python, fortran, C++

BioinformaticsMolecular modelingComputer-aided drug discoveryDevelopment of molecular modeling softwareMachine learning (deep learning)

Molecular dynamics simulations for biomolecular system - MD simulations combined with hydration free energy calculation for simple proteins using 3D-RISMs- Calculation of binding free energy protein-protein complex (synthetic peptide inhibitor for MDM2) using MD simulations and 3D-RISMs- Water dynamics surrounding spin-labelling compounds using MD simulations

- Development of template-based protein-protein complex modeling algorithm- Structural modeling of cases for protein-protein & protein-peptide structures in CAPRIs - Development of knowledge-based potential for macromolecular structure modelingParallel programming in massive supercomputing clusters

Drug Discovery Team- Structure-based Drug Discovery- Systems Biology