Research Programmer · Computational Biologist/Biophysicist
Bridging biomolecular physics, cell & molecular biology, biochemistry, and computer science

• 🔬 Decode complex biological phenomena at molecular & cellular levels
• 🧬 Design proteins, antibodies, vaccines & small molecules
• ⚡ Automate and optimize scientific workflows for rapid discovery
• 🦠 Unravel pathogen–host interactions at molecular and cellular scales

• Biological Data Sciences: Python · R · SQL · pandas · SciPy · scikit-learn
• Structural Bioinformatics: AlphaFold · ColabFold · Boltz-1 · ProteinMPNN · Rosetta
• Computational Biophysics: WT-MetaD · OPES · GaMD · ABF/eABF · Umbrella Sampling · FEP

• FEMWgen: Automated window generation for eABF/ABF & Umbrella Sampling, accelerating free-energy workflows.
• MSTBx: Toolbox for rapid system preparation: molecular dynamics setups, free-energy calculations, and method switching with Slurm integration.
• CompBiology-Biophysics: End-to-end pipelines for MD analysis, free-energy estimation, and reproducible research.
• Jarzynski: Non-equilibrium MD implementations to compute PMFs & binding free energies using the Jarzynski Equality.

🚀 Browse all repositories: github.com/groponp

1. Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening & MD approach
   Journal of Biomolecular Structure and Dynamics 38(11), 3225–3234 (2020)
2. Novel multi-epitope protein vaccine candidate for Leishmania species: immunoinformatics & MD
   Computational Biology and Chemistry 83, 107157 (2019)
3. In silico inhibitory activity of C. rotundus phytomolecules against VacA
   Journal of Biomolecular Structure and Dynamics 41(20), 10713–10724 (2023)
4. Virtual screening & MD of natural inhibitors for serine/threonine kinase 16
   Molecular Diversity (2024) · 7 citations

_{Citations: 56 · h-index: 5 · i10-index: 1}

Open to collaborations with:

• 💊 Pharma & Biotech: drug design, lead optimization, vaccine development
• 🧪 Academic & Industrial Research Groups: computational/theoretical biophysics, systems biology
• 🤖 Interdisciplinary Teams: combining physics, biology, AI & data science

• 📧 Email: [email protected]
• 🐦 Twitter: @roponpallab
• 🎓 Google Scholar: Google Scholar Profile

🌟 "Building computational tools to explore molecular and cellular complexity and drive therapeutic discovery." 🌟