Principal Scientist – Computational Protein Design & Engineering

PharmaEssentia U.S.A. • Bedford, MA

88d

About The Position

PharmaEssentia is a global biopharmaceutical company committed to developing innovative therapies that address unmet medical needs in oncology, hematology, and immunology. With a strong foundation in disease biology, biologics, and translational science, we are expanding our research capabilities to drive the next wave of therapeutic breakthroughs. The PharmaEssentia Innovation Research Center (PIRC) is seeking a highly motivated and collaborative Principal Scientist – Computational Protein Design & Engineering to join our Biologics Platform team. Our platform integrates protein engineering, antibody discovery, and immune cell modulation to deliver transformative therapies. The ideal candidate will possess deep expertise in computational methods to advance the design and innovation of multi-specific Biologics. They will spearhead the development of advanced computational strategies for biologics discovery, working closely with Biologics Platform team members to implement an integrated approach combining computational methods, rational design, and display library-based techniques for protein engineering. Together, we will drive the next wave of novel bi- and tri-specific therapeutic modalities.

Requirements

• Ph.D. in Computational Protein Design, Structural Biology, Protein Engineering, or a related field, with 6+ years of industry experience applying computational modeling to protein design and antibody engineering, and a proven track record of contributing to therapeutic development.
• Proficiency with leading modeling tools such as AlphaFold, RoseTTAFold, ProteinMPNN, MOE, or Schrödinger.
• Expert in leveraging structural modeling, epitope prediction, repertoire mining, protein language models, and AI/ML techniques to accelerate the discovery and optimization of novel therapeutic candidates.
• Demonstrated leadership in advancing discovery programs from lead identification through preclinical development.
• Experience with diverse antibody formats, including VHHs, multi-specifics, T cell receptors (TCRs) and T cell engagers.

Nice To Haves

• Expertise in the design and development of CD3-based bispecific and tri-specific T cell engagers, with a focus on enhancing selectivity, potency, and safety.
• Experience with NGS immune repertoire analysis and data interpretation.

Responsibilities

• Lead the development and application of advanced AI/ML models and computational structure- and sequence-based tools to design, engineer, and optimize biologics—including antibodies, cytokines, T cell engagers, and multi-specific modalities.
• Utilize in silico approaches to guide structure prediction, paratope/epitope mapping, affinity maturation, stability and developability assessments, and the design of display libraries to support lead identification and optimization.
• Stay abreast of emerging advancements in machine learning and computational protein design and establish strategic frameworks to drive innovation in biologics engineering.
• Initiate and champion novel program concepts with the potential to evolve into pipeline assets.
• Collaborate with CROs, external partners, and internal teams on protein expression, purification, macromolecular interaction studies, and cell-based functional assays to identify development candidates.
• Foster a culture of transparency, innovation, and high performance—grounded in collaboration, engagement, ownership, accountability, and inclusion.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree