Senior Scientist, Computational Chemistry

Magnet Biomedicine, Inc.; Boston (MA); On-site; USD 145,000 - 185,000; Full time

Job summary

Magnet Biomedicine, Inc. seeks a highly capable Computational Chemist to accelerate drug discovery using cutting‑edge AI/ML and structure‑based design. You will work at the intersection of cheminformatics, data science, and methods to advance the molecular glue platform.

You will collaborate across disciplines—medicinal chemistry, biology, proteomics, and informatics—to drive the DMTA cycle and develop scalable computational tools and workflows. A PhD with strong publication history is preferred.

Qualifications

• : Ph.D. in Computational Chemistry, Cheminformatics, Chemistry, Computer Science, Data Science, or related field with 5–8 years in life sciences; or equivalent experience
• : Demonstrated expertise in ligand‑ and structure‑based computational drug design and optimization
• : Hands‑on experience with Vortex, Schrödinger Suite, MOE, and/or AWS; familiar with AMBER, Gromacs, NAMD, VMD
• : Excellent written and verbal communication skills for diverse audiences
• : Ability to manage multiple priorities in a fast‑paced environment
• : Proficiency in Python and cheminformatics/data science packages (RDKit, Scikit‑learn, Pandas, NumPy) in Linux
• : Track record of publications, patents and conference presentations in drug discovery

Responsibilities

• Apply ligand‑ and structure‑based drug design approaches to enable hypothesis‑driven compound design and library design
• Collaborate with medicinal chemists, biologists, biophysicists, protein scientists, proteomics, DMPK, and informatics teams to support early discovery
• Communicate findings clearly to technical and non‑technical audiences across the organization
• Build and maintain computational tools, workflows, AI/ML models, and databases for processing complex drug discovery data
• Analyze and interpret experimental data to generate actionable insights guiding the DMTA cycle
• Drive development of novel computational methodologies including AI/ML, data exploration, and visualization
• Manage and maintain R&D software platforms (Vortex, Schrödinger Suite, MOE, RESTful APIs)

Skills

Python

Cheminformatics

Data science

Linux

RDKit

Scikit-learn

Pandas/Numpy

Communication

Education

Ph.D. in Computational Chemistry/Cheminformatics/Related field

Tools

Vortex

Schrödinger Suite (Maestro, LiveDesign, PyMOL)

MOE

AWS

AMBER

Gromacs

NAMD

VMD

Job description

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.
• 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.
• Demonstrated expertise in ligand‑based and structure‑based computational drug design and optimization.
• Hands‑on experience with Vortex, Schrödinger Suite (Maestro, LiveDesign, PyMOL), MOE, and/or AWS, and familiar with AMBER, Gromacs, NAMD, VMD.
• Excellent written and verbal communication skills, with a proven ability to present complex scientific concepts to diverse audiences.
• Ability to manage multiple priorities independently in a fast‑paced, dynamic environment.
• Proficiency in Python and relevant cheminformatics/data science packages (e.g., RDKit, Scikit‑learn, Pandas, NumPy); comfort working in a Linux environment.
• Strong analytical and problem‑solving skills with the ability to derive meaningful insights from complex, multi‑dimensional datasets.
• A track record of publications, patents and conference presentations in drug discovery.

Preferred

• Experience with molecular glues, PROTACs, RIPTACs, or other heterobifunctional degrader or non‑degrader modalities.
• Familiarity with FEP, molecular dynamics and medicinal chemistry design principal.
• Experience with DEL data analysis workflows and target/presenter pair prediction.
• Familiarity with cheminformatics and cofolding tools, 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.

$145,000—$185,000 USD