Computational Biologist | Protein & Peptide Design | AI/ML | Molecular Modeling | Multiscale Molecular Dynamics Simulations
Final Stage PhD researcher at IIT (BHU) working at the interface of computational protein design, AI/ML, structural bioinformatics, molecular modeling, and multiscale molecular dynamics.
Research interests: Protein & peptide design · Sequence–structure modeling · Molecular docking · Molecular dynamics · Free-energy analysis · AI/ML for biomolecules
Computational toolkit: Python · PyTorch · R · GROMACS · ProteinMPNN · AlphaFold · ESMFold · MOE · HDOCK · Rosetta · PyMOL · VMD · Chimera · NAMD
- AI-assisted protein and peptide sequence design
- Structure-guided biomolecular redesign
- Sequence–structure–function analysis
- Protein–protein and protein–peptide interactions
- Molecular docking and interface analysis
- All-atom and coarse-grained molecular dynamics
- Simulation-guided candidate prioritization
🔬 AI/ML for Protein Design
LSTM-based sequence prediction and structure-informed sequence design.
🧬 Structure-Guided Protein Redesign
ProteinMPNN-assisted sequence generation, Rational-redesign, interface engineering, and candidate prioritization.
⚛️ Molecular Modeling & Simulation
GROMACS-based AAMD/CGMD workflows, conformational analysis, and free-energy calculations.
🧪 Computational Bioinformatics
Sequence analysis, structural bioinformatics, biological data processing, and statistical analysis.
My Ph.D. research has resulted in 7 peer-reviewed publications and 3 book-chapters spanning computational protein design, molecular simulation, structural bioinformatics, antibody and nanobody redesign and biomolecular engineering.
📄 Google Scholar
🔗 ORCID
💼 LinkedIn
📧 amarjeetyadav.rs.bce23@iitbhu.ac.in | amarjeetyadav1072000@gmail.com 📍 IIT (BHU), Varanasi, India