PP

Prabakaran Ponraj

Institute for Protein Innovation, Moderna Therapeutics (United States), Bharathidasan University, Sanofi Genzyme

ORCID iD 0000-0002-4049-4813
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About

EXECUTIVE SUMMARY
Computational biologics leader with 20+ years integrating antibody science, structural biology, and AI/ML to accelerate biologics discovery from target to clinic. Expertise spans antibody discovery and engineering, structure determination, NGS-enabled display and microfluidics screening, immune repertoire analytics, multispecifics, VHHs, and T-cell engagers. Conceived and delivered an in-silico antibody design platform at Sanofi and computationally designed a CD4 inhibitor (patented, NIH Tech Transfer Award), licensed by Gilead and advanced to Phase I as the CD4 component of a bispecific T-cell engager (amtabafusp alfa, GS-8588). Authored 75+ publications, determined the first SARS-CoV antibody-antigen complex structure (PDB: 2DD8), and developed a PDB-wide structural classification of protein-DNA complexes (Structure 2006; featured in an accompanying Structure Preview). Develops and applies AlphaFold2-Multimer, ESM, ProteinMPNN, Boltz-2, and protein/antibody language models to next-generation biologics design. Deployed and modeled complex structure predictions with AF2-Multimer and Boltz-2 on Lambda Cloud, and managed PyTorch/JAX model components, resolving mismatches and integration issues, in support of sequence-structure and sequence-function modeling of biomolecular interactions.

CORE COMPETENCIES
AI-Driven Protein & Biologics Design | De Novo Antibody Design | Generative Models (GANs, VAEs) | Antibody Discovery & Engineering | Structural Biology & Antibody-Antigen Structure Determination | Protein-DNA & Protein-Protein Interaction Analysis | Protein Engineering & Multispecifics | VHH & Novel Antibody Modalities | Immune Repertoire Analysis & Immunogenomics | Computational Biology & Bioinformatics | Protein Language Models (PLMs) | Sequence-Structure-Function Modeling | PyTorch/JAX | HPC & Cloud (Lambda Cloud) | Agentic AI-Assisted Development (Claude Code, Codex) | Platform Development | Scientific Leadership & Innovation

Employment

  • Institute for Protein Innovation Associate Director, Computational Biology & Bioinformatics
    2025 - 2026
  • Moderna Therapeutics (United States) Consultant
    2024 - 2025
  • Sanofi Genzyme Senior Principal Scientist, AI Innovation
    2018 - 2024
  • Intrexon Corp Germantown Senior Scientist
    2015 - 2018
  • Sanofi Pasteur Contractor
    2014 - 2015
  • Leidos Inc Frederick Scientist I
    2009 - 2014
  • Duke University Senior Scientist
    2007 - 2009
  • National Institutes of Health Post-doctoral Visiting Fellow
    2002 - 2007
  • RIKEN Post-doctoral, STA Fellow
    1999 - 2002

Education

  • Bharathidasan University PHD (X-ray Crystallography)
    1994 - 1998

Projects & Funding

Projects & funding information is unavailable.

Publications (80)