Computational Biology & ML Engineer – Peptide & Protein and chemical Design
Location: India (Remote/Hybrid)
Engagement: Full-time long-term contract
We are building an AI-enabled platform for designing and evaluating small molecules, peptide and folded protein binders. We are looking for a senior, hands-on individual contributor who can serve as both the technical lead and scientific subject matter expert for this initiative.
This is not a purely academic or software-engineering role. The successful candidate must be able to design the scientific approach, Use AI to output production-quality code, test the complete workflow, and evaluate whether the results are biologically meaningful.
Key responsibilities
Build and validate end-to-end peptide and protein-design pipelines, from target preparation and candidate generation through structural verification and ranking.
Integrate tools such as BoltzGen, Boltz-2, Protenix, Reinvent 4,P2Rank, inverse-folding models, and protein-interface analysis methods.
Develop Python-based services for sequence generation, filtering,



diversity selection, GPU-based inference, data capture, and reporting.
Design, train, and benchmark target-conditioned ML models using distillation, uncertainty estimation, applicability checks, and active-learning methods.
Establish scientific and software testing, including hard negatives, held-out target families, false-negative controls, reproducibility, throughput, and GPU-cost benchmarks.
Act as the primary scientific advisor to product, engineering, and experimental teams.
Required background
Advanced degree or equivalent experience in computational biology, bioinformatics, structural biology, machine learning, or a related field. Muster is a must.
At least 2 years of organizational work experience is a must.
Solid knowledge of small chemical molecules, peptide design, protein structure, protein-protein interfaces, and computational protein design.
Python and practical experience with PyTorch or JAX

📌 Computational Biology (India)
🏢 Pattern Agentix
📍 India