👋 Hello, I'm Georcki Ropón-Palacios (@groponp)

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

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🧑‍💼 About Me

• 🔬 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

🔑 Key Areas

• 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

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🚀 Core Expertise

Domain	Tools & Technologies
Molecular Simulations	GROMACS · NAMD · AMBER · CHARMM · PLUMED · OpenMM
Enhanced Sampling & Free Energy	WT-MetaD · eABF/ABF · Umbrella Sampling · OPES · GaMD · FEP
Scientific Programming & HPC	Python · Fortran · Bash · Snakemake · Nextflow · Dask · MPI · SLURM · Apptainer · Docker
Structure Prediction & Design	AlphaFold2/3 · ColabFold · Boltz-1 · ProteinMPNN · RFDifussion
Data Science & Analysis	MDAnalysis · mdtraj · pytraj · pandas · NumPy · SciPy · scikit-learn
Visualization	PyMOL · ChimeraX · VMD · matplotlib · Plotly
Cloud & Networking	AWS

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🌟 Featured Projects

• 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

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📚 Top Publications

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}

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🤝 Collaborations & Opportunities

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

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📬 Let's Connect

• 📧 Email: groponp@gmail.com
• 🐦 Twitter: @roponpallab
• 🎓 Google Scholar: Google Scholar Profile

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