Top 78 Computational chemistry Jobs in Boston, Ma

Senior Director, AIRx Computational Chemistry
Takeda Pharmaceutical —Boston, MA
- $212,000 - $333,190 a year
- Full-time
- Hybrid work
- 11+ years
- Doctor of Philosophy
- Senior level
- Paid holidays
- Disability insurance
Scientist II, Discovery Chemistry and Automation (Parallel Synthesis)
Valo Health —Lexington, MA
- $123,250 - $145,000 a year
- 6 years
- Bachelor of Science
- Bachelor's degree
- Retirement plan
6d
Principal Scientist, Medicinal Chemistry
C4 Therapeutics Inc —Watertown, MA
- $181,012.05 - $200,066.00 a year
- Full-time
- Management
- Doctor of Philosophy
- Senior level
Quick Apply
Computational Biomedical Research Scientist
Delta Search Labs —Cambridge, MA
- Email
- Computer science
- Computer Science
- Analysis skills
Senior Scientist, Discovery Chemistry
Sarepta Therapeutics —Bedford, MA
- $112,000 - $140,000 a year
- Full-time
- Management
- 5 years
- Analysis skills
Scientific Software Developer II – Modeler
Cadence Design Systems —Boston, MA
- $101,500 - $188,500 a year
- Full-time
- Mid-level
- C++
- Doctor of Philosophy
- Employee stock purchase plan
- Paid holidays
Senior Scientist, Proteomics
Flagship Pioneering, Inc. —Cambridge, MA
- $126,000 - $159,500 a year
- Doctor of Philosophy
- Senior level
- 4 years
- Retirement plan
Head of Automated Small Molecule Synthesis
Takeda Pharmaceutical —Boston, MA
- $177,000 - $278,080 a year
- Full-time
- Bachelor of Science
- Bachelor's degree
- Doctor of Philosophy
- Paid holidays
- Disability insurance
Research Senior Scientist, Cheminformatics
Takeda Pharmaceutical —Boston, MA
- $137,000 - $215,270 a year
- Computer Science
- Doctor of Philosophy
- Senior level
- Paid holidays
- Disability insurance
Research Senior Scientific Director, Head of Hit ID and Sample Management (Automation)
Takeda Pharmaceutical —Boston, MA
- $212,000 - $333,190 a year
- Hybrid work
- Bachelor of Science
- 11+ years
- Presentation skills
- Paid holidays
- Disability insurance
Formulation Laboratory Technician
On-Board Companies —Marlborough, MA
- $26.65 an hour
- Email
- Mid-level
- Master's degree
- Analysis skills
- Health insurance
- Dental insurance
Quick Apply
Director, Analytical Chemistry
Moderna, Inc. —Cambridge, MA
- $167,000 - $300,700 a year
- Full-time
- Doctor of Philosophy
- In-person
- Senior level
- Health insurance
- Paid time off
Data Scientist Contractor, Computational Biology
CAMP4 Therapeutics —Cambridge, MA
- Contract
- Mid-level
- 3 years
- AWS
Quick Apply
10d
Associate Principal Scientist, Molecular Modeling
Merck —Boston, MA
- $142,400 - $224,100 a year
- Full-time
- Bachelor of Science
- Bachelor's degree
- Doctor of Philosophy
- Paid holidays
- Health insurance
10d
Scientist, Biochemistry
HotSpot Therapeutics —Boston, MA
- Full-time
- Bachelor of Science
- Project management
- Bachelor's degree
- Paid holidays
Staff Computational Biologist
Valo Health —Lexington, MA
- $165,750 - $230,100 a year
- Hybrid work
- Computer science
- Azure
- Computer Science
- Retirement plan
Scientist I – Fischer Lab
Dana-Farber Cancer Institute —Boston, MA
- $80,000 - $95,900 a year
- Full-time
- Doctor of Philosophy
- Mentoring
- In-person
Mass Spectrometry Scientist
Convergent Research —Watertown, MA
- $86,000 - $119,000 a year
- Full-time
- 5 years
- Master's degree
- Doctor of Philosophy
- Paid parental leave
- AD&D insurance
5d
Sr Scientist/Principal Scientist - Genomics Sciences
Eli Lilly —Boston, MA
- $71,250 - $187,000 a year
- Full-time
- Master's degree
- Bachelor's degree
- Continuous improvement
- Health insurance
- Dental insurance
8d
Scientist I, In Vitro Pharmacology
Flagship Pioneering, Inc. —Boston, MA
- $100,000 - $126,500 a year
- Mid-level
- Doctor of Philosophy
- Retirement plan

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computational chemistry jobs near boston, ma

Senior Director, AIRx Computational Chemistry

Takeda Pharmaceutical -
Boston, MA

Apply Now

Job Details

Full-time
$212,000 - $333,190 a year

Benefits

Paid holidays
Disability insurance
Health insurance
Dental insurance
Tuition reimbursement
Paid time off
Vision insurance
401(k) matching
Volunteer time off
Life insurance

Qualifications

Computational research
Molecular dynamics simulations
Simulation modeling (chemistry)
Drug discovery
Model deployment
Simulation tools
Bioinformatics tools
Pharmaceutical research
Python

Full Job Description

By clicking the “Apply” button, I understand that my employment application process with Takeda will commence and that the information I provide in my application will be processed in line with Takeda’s Privacy Notice and Terms of Use. I further attest that all information I submit in my employment application is true to the best of my knowledge.

Job Description

Senior Director, Computational Chemistry

Takeda Research is constructing the Discovery Automation & Robotics (DAR) group built on AI, automation, new ways of working, and talent with the singular vision of delivering differentiated medicines to the clinic at speed and cost. To catalyze these efforts, Takeda is creating two complementary units: AI Research Accelerator (AIRx) and The Discovery Automation & Robotics (DAR) group.

AIRx will consist of a dedicated group of experienced drug hunters with the autonomy of a biotech and the resources of a leading pharmaceutical company. It is designed to incubate the future AI-powered operating models and deliver candidates to the clinic at industry leading speed and success rates.

Purpose

Reporting to the Head of AIRx, the AIRx Computational Chemist sits at the scientific heart of AIRx's AI-first operating model. This role drives in silico molecular design, leverages predictive models, and applies generative chemistry to power rapid DMTA cycles — directly enabling the speed and precision that define the AIRx incubator In AIRx, computational chemistry is a first-order decision-making function — generative proposals from this role directly shape what gets synthesized, what gets deprioritized, and ultimately what reaches the clinic. The role is deeply hands-on, with a unique opportunity to directly shape candidates that advance to the clinic through close collaboration with the wider AIRx design team.

Accountabilities

Apply generative AI, structure-based design, free energy perturbation, and predictive ML models to design and prioritize chemical matter
Partner closely with Medicinal Chemists to translate computational outputs into actionable synthesis priorities; challenge and be challenged in equal measure
Lead and oversee virtual screening campaigns, ADMET predictions, and selectivity assessments to inform and accelerate design decisions
Contribute to building and refining AI/ML model training datasets from AIRx experimental outputs
Develop and maintain computational workflows that increase team speed and reproducibility
Interpret and integrate structural biology data (X-ray, cryo-EM) into computational design strategies
Communicate complex computational findings clearly to cross-disciplinary colleagues and governance forums
Stay current with advances in generative AI, protein structure prediction, and ML methods; proactively apply new approaches

Qualifications & Competencies

PhD in computational chemistry, cheminformatics, biophysics, or closely related discipline
12–15+ years of drug discovery experience with demonstrated track record of computational impact on programs
Proficiency across computational tools: molecular docking, MD simulation, FEP, QSAR/ADMET modeling
Strong coding skills (Python required); experience building and deploying ML models in a drug discovery context
Experience with structure-based drug design; ability to interpret crystallography or cryo-EM data
Experience applying generative AI or large language models to molecular design preferred
Collaborative, communicative, and comfortable at the wet/dry scientific interface

ADDITIONAL INFORMATION

The position will be based in Cambridge, MA. This position is currently classified as “hybrid” by Takeda’s Hybrid and Remote Work policy

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices.

For Location:

Boston, MA

U.S. Base Salary Range:

$212,000.00 - $333,190.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location.

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation.

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Full time

Job Exempt

Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.

Apply Now

Refine Your Search

computational chemistry jobs in boston, ma

Senior Director, AIRx Computational Chemistry

Scientist II, Discovery Chemistry and Automation (Parallel Synthesis)

Principal Scientist, Medicinal Chemistry

Computational Biomedical Research Scientist

Senior Scientist, Discovery Chemistry

Scientific Software Developer II – Modeler

Senior Scientist, Proteomics

Head of Automated Small Molecule Synthesis

Research Senior Scientist, Cheminformatics

Research Senior Scientific Director, Head of Hit ID and Sample Management (Automation)

Formulation Laboratory Technician

Director, Analytical Chemistry

Data Scientist Contractor, Computational Biology

Associate Principal Scientist, Molecular Modeling

Scientist, Biochemistry

Staff Computational Biologist

Scientist I – Fischer Lab

Mass Spectrometry Scientist

Sr Scientist/Principal Scientist - Genomics Sciences

Scientist I, In Vitro Pharmacology

I want to receive the latest job alert for computational chemistry in boston, ma

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