Job Description
Role: Protein Engineering Scientist (AI-Driven Large
Molecule Design)
Location: Science & Technology Park / Venture Center, Pune, Maharashtra
Work Mode: Hybrid/Remote- 6 days
Role Overview
We are looking for a Protein Engineering Scientist with strong hands-on experience in computational protein design and large molecule engineering.
This role focuses on:
● protein and enzyme engineering
● antibody and binder design
● AI-driven structure and sequence generation
● end-to-end large molecule design workflows
You will work at the intersection of biology, AI, and computational modeling to design and optimize next-generation protein therapeutics and engineered biomolecules.
What You’ll Work On
● Designing and optimizing proteins, enzymes, antibodies, and other large molecules for specific functional outcomes
● Working on end-to-end protein engineering workflows from sequence to structure to function
● Applying AI-driven approaches for protein structure prediction and design
● Designing mutations to improve stability, binding affinity, specificity, and activity
● Analyzing protein-protein and protein-ligand interactions
● Integrating generative AI models into protein and enzyme engineering pipelines
● Working with evolving toolchains and adapting to new methods in AI-driven protein design
● Collaborating with cross-functional teams across computational and experimental domains
Key Responsibilities
● Execute protein engineering workflows including sequence design, structure prediction, and optimization
● Work with advanced AI-driven tools such as RFdiffusion, AlphaFold 3, ProteinMPNN, and Boltz-2
● Leverage additional emerging tools and frameworks in protein and large molecule design as required
● Design and evaluate enzyme variants and antibody candidates for therapeutic and industrial applications
● Analyze structural outputs to assess stability, folding, and binding interactions
● Develop and refine computational pipelines for large molecule and protein engineering
● Collaborate with AI/ML and backend teams to integrate protein design workflows into scalable systems
● Interpret computational outputs and translate them into actionable biological insights
Tech Stack
● Protein & Large Molecule Design: RFdiffusion, AlphaFold 3, ProteinMPNN, Boltz-2, and other emerging tools
● Molecular Modeling: PyMOL, Chimera, docking and structural analysis tools
● Simulation (Preferred): MD tools such as GROMACS, OpenMM
● Programming: Python (NumPy, Biopython, PyTorch preferred)
● Other: Sequence analysis tools, structural biology toolkits
What We’re Looking For
Core Domain Expertise
● Strong understanding of protein engineering and large molecule design workflows
● Hands-on experience in enzyme engineering, antibody design, or protein therapeutics
● Deep understanding of protein structure-function relationships
● Familiarity with stability, folding, and interaction analysis AI-Driven Protein Design (Critical)
● Hands-on experience with modern AI-based protein design tools such as RFdiffusion, AlphaFold 3, MPNN-based methods, and related systems
● Understanding of generative approaches for protein structure and sequence design
● Ability to work with evolving AI toolchains in protein engineering
Computational & Technical Skills
● Proficiency in Python for scientific computing
● Experience with structural biology and molecular modeling tools
● Ability to work with computational pipelines and large biological datasets
Nice to Have
● Experience with molecular dynamics simulations
● Exposure to wet-lab validation workflows or experimental collaboration
● Experience in therapeutic protein or enzyme optimization pipelines
● Experience working in interdisciplinary AI + biology environments
Eligibility:
● Master’s or PhD in Biotechnology, Bioinformatics, Computational Biology, Structural
Biology, or related field
● 1–5 years of hands-on experience in protein engineering / enzyme engineering / antibody design
Note: Exceptional candidates with strong project work or research experience in protein engineering and AI-driven design will also be considered.
