I develop computational methods and reproducible workflows for molecular dynamics, de novo molecular design, QSAR modeling, with a focus on practical drug-discovery applications.
I am the lead developer of StreaMD, an open-source toolkit for automated molecular dynamics workflows at scale, and of CReM-opt and CReM-agent, docking-guided frameworks for de novo molecular design and optimization.
Skills
Programming
- Python
- Bash
- R
- Cython
- SQL
- LaTeX
Drug discovery and CADD
- molecular docking
- molecular dynamics simulations
- binding free-energy calculations (MM/GBSA, MM/PBSA, FEP, ABFE)
- QSAR
- de novo molecular design
- protein-ligand interaction analysis
- automated preprocessing and quality control of chemical datasets
Modeling and cheminformatics software
- RDKit
- MDAnalysis
- ProLIF
- CReM
- GROMACS
- OpenMM
- Amber
- AutoDock Vina
- Gnina
- Glide and Maestro
- gmx_MMPBSA
- A3FE
- ChemFP
- Gaussian
- MCPB.py
- PyMOL
- Chimera
Python ecosystem
- scikit-learn
- pandas
- NumPy
- Matplotlib
- Plotly
- Streamlit
High-performance computing
- Dask
- PBS
- SLURM
- multiprocessing
- GNU parallel
- code performance profiling
Software development
- Git and GitHub
- package distribution (PyPI, conda-forge)
- environment management (conda, venv)
- containerization (Docker, Apptainer)
- REST API design
- reproducible workflows
- unit and integration testing
LLMs and AI agents
- agent-driven scientific workflows
- hosted and local open-source LLMs
- prompt design
- tool integration
- structured agent-tool communication