Aditi Khankhoje

About Aditi Khankhoje

I work at the intersection of protein science and cutting-edge AI to push the boundaries of what is possible in enzyme engineering.Grounded in classical engineering methodologies including structure-guided rational design, iterative mutagenesis, and directed evolution, I have systematically optimised enzyme activity across multiple protein targets at Atlas Data Storage and Amyris, achieving consistent 2–3 fold improvements in catalytic performance. This foundation in sequence–structure–function relationships remains central to how I approach every engineering challenge.The transformative shift in my work has come through the adoption of deep learning-based protein design frameworks. By integrating generative models, including ProteinMPNN for sequence design, RFdiffusion for backbone generation and structure-guided design, and FireProt for thermostability optimisation, I have driven 200–300 fold improvements in recombinant protein expression, a step-change that has significantly accelerated engineering cycles and expanded the design space we can explore.At Atlas Data Storage, I apply this integrated approach to a high-value enzyme engineering programme, leveraging both wet-lab validation and in silico optimisation to de-risk candidates earlier in the pipeline and deliver robust, scalable outcomes.I am particularly interested in connecting with and learning from scientists and engineers working at the frontier of AI-assisted protein design, directed evolution, and computational biophysics.

Experience

1. Senior Scientist

   Atlas Data Storage

   May 2025 — Present · South San Francisco, CA, US

Education

• Department of Pharmaceutical Sciences, RTM Nagpur University

  Bachelor of Pharmacy (B.Pharm.), Pharmacy

  2007 — 2011

• University of Delaware

  Master of Science (MS), Chemistry and Biochemistry

  2012 — 2015

Skills

• Sql
• Western Blotting
• Drug Discovery
• Biochemistry
• Homology Modeling
• Pharmacology
• Cell Culture
• Bioinformatics
• Molecular Biology
• Research
• Patient Education
• Immunohistochemistry
• Pcr
• Fluorescence Polarization Assay
• Chemistry
• High-Performance Liquid Chromatography (Hplc)
• Radioactive Waste Management
• Preclinical Trials
• Akta
• Scientific Communications
• Hplc
• Radioimmunoassay
• Dna Extraction
• Dna
• Biotechnology
• Protein Purification
• Crispr
• Protein Engineering
• Dna Sequencing
• Graphpad Prism
• Enzyme Kinetics