Senior Scientist - Computational Chemistry

About Magnet Biomedicine

Magnet is a biotechnology company pioneering the discovery of oral molecular glues - small molecules that induce proximity between proteins to modulate their function. Our proprietary TrueGlue(TM) platform is designed to address hard-to-drug targets across cancer and immune-mediated diseases.

With support from ARCH Venture Partners, Newpath Partners, Taiho Ventures, and Eli Lilly, Magnet is advancing internal programs in oncology, immunology, and inflammation. Magnet has also entered into a collaboration and license agreement with Eli Lilly to discover, develop, and commercialize specific molecular glue therapeutics in oncology.

Position Summary

We are seeking a highly motivated and hands-on Computational Chemist  to join our team. In this role, you will apply cutting-edge computational methods and AI/ML approaches to accelerate drug discovery from hit identification through clinical candidate nomination. You will be a key contributor to our molecular glue platform, working at the intersection of structure-based design, cheminformatics, and data science to drive the DMTA cycle forward.

This is a highly collaborative role that requires both deep technical expertise and the ability to translate scientific questions into actionable strategies across multidisciplinary teams.

Responsibilities

• Apply ligand-based and structure-based drug design approaches (including molecular dynamics simulation, TI/FEP+, water analysis, protein dynamics, etc) to enable hypothesis-driven compound design and reaction-based library design.
• Partner closely with medicinal chemists, biologists, biophysicists, protein scientists, proteomics, DMPK, and informatics teams to support early discovery and pipeline programs.
• Apply medicinal chemistry design principles (SAR, potency and property balance, ADMET, selectivity, and synthetic feasibility) to prioritize and refine computational designs.    
• Communicate findings clearly and compellingly to both technical and non-technical audiences across all levels of the organization.
• Build and maintain computational tools, workflows, AI/ML models, and databases for the processing and analysis of complex drug discovery datasets, including DNA-encoded library (DEL) data analysis, DEL library construction, druggability evaluation, target/presenter gluability and ADMET prediction.
• Analyze and interpret experimental data (such as ternary and binary biochemical, biophysical and cellular assay data, X-ray/Cryo-EM structures, XL-MS/HDX/NMR, DEL data, proteomics screening) to generate actionable insights that guide project decisions and impact the design-make-test-analyze (DMTA) cycle.
• Drive development and implementation of novel computational methodologies — including AI/ML, data exploration, and visualization to strengthen and expand our molecular glue discovery platform.
• Manage and maintain R&D software platforms including Vortex, Schrödinger Suite (Maestro, LiveDesign, PyMOL), MOE, and RESTful APIs.

Qualifications

Required

• Ph.D. in Computational Chemistry, Cheminformatics, Chemistry, Computer Science, Data Science, or a related field, with 5-8 years of experience in life sciences; or equivalent combination of education and experience.
• A track record of publications, patents and conference presentations in drug discovery.    
• Proficient in ligand-based and structure-based drug design approaches (including docking, reaction enumeration, pharmacophore hypothesis generation, molecular dynamics, FEP, etc) to enable hypothesis-driven compound design and library synthesis.
• Hands-on experience with Vortex, Schrödinger Suite, MOE, AMBER and open source tools.
• Solid understanding of medicinal chemistry design principles and project data in drug discovery.
• Demonstrated track record of independently generating and proposing original compound design ideas (new scaffolds, substituents, linkers, and optimization strategies). 
• Proactive problem-solver with strong curiosity and a drive to learn.
• Demonstrated partnership with medicinal chemists and biologists across iterative DMTA cycles.
• Excellent written and verbal communication skills, with a proven ability to present complex scientific concepts to diverse audiences.

Preferred

• Experience with molecular glues, PROTACs, DEL data analysis, RIPTACs, or other heterobifunctional degrader or non-degrader modalities.    
• Familiarity with cheminformatics and Agentic AI, explainable AI (xAI), generative AI such as REINVENT, LiblNVENT.
• Experience building scalable research infrastructure with automation, good design patterns, and reusability in mind.

National salary range. Salary will be determined by many factors, including but not limited to, specific competencies, relevant education, qualifications, certifications, experience, skills, performance, location and business or organizational needs. 145000 - 185000 USD