16 Computational Chemistry jobs in the United States

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**
Job Posting Description
At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.
**Objective / Purpose:**
+ As a Computational Chemistry Scientist, you will work as part of a multi-disciplinary team of Medicinal Chemists, Computational Chemists, Data Scientist, Structural Biologists, Pharmacologists and Biologists to provide Computational expertise to advance drug discovery projects
+ Contribute to drug discovery efforts across various modalities including small molecules, bifunctional degraders, peptides, RNA/oligonucleotides, and biologics
+ Implement and execute innovative computational methodologies and tools such as AI approaches to support drug discovery efforts
**Accountabilities:**
+ Demonstrate expert understanding of computational chemistry principles and their application within a multidisciplinary drug discovery environment
+ Identify, develop, validate, and implement innovative computational approaches that improve research productivity and success
+ Provide crucial technical knowledge and input to project teams to drive decision-making in drug discovery projects
+ Build and develop a strong team of Computational Chemists to high productivity levels
+ Demonstrate leadership and enterprise thinking in managing multi-disciplinary team
**DIMENSIONS AND ASPECTS:**
+ Expertise in a variety of computational tools and methodologies including docking, virtual screening, molecular dynamics, free energy perturbation, homology modeling, quantum mechanics, pharmacophore elucidation, data mining, machine learning, cheminformatics, clustering, similarity & diversity analysis
+ Significant Industry experience contributing as Computational Chemist on drug discovery projects
+ Strong Impact in progressing Discovery Projects from Hits to Clinical Leads
+ Extensive knowledge & experience in using a variety of tools for Hit ID
+ Provide project teams with computational strategies to inform, influence, and prioritize compound designs for potency/selectivity and improve ADME/Tox endpoints
+ Ability to effectively integrate emerging generative chemistry methods and other modern machine learning and artificial intelligence (AI) applications in small molecule drug discovery
+ Proficiency with state-of-the-art Computational Chemistry software
+ Network with renowned researchers in computational chemistry/AI
**EDUCATION, BEHAVIOURAL COMPETENCIES AND SKILLS:**
+ PhD degree in a relevant scientific discipline
+ 2+ years of Industry (pharma/biotech) drug discovery experience required
**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:**
$137,000.00 - $215,270.00
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.

Our client, a cutting-edge biotechnology firm at the forefront of pharmaceutical discovery, is seeking a highly accomplished Principal Scientist, Computational Chemistry to lead innovative research in **Austin, Texas, US**. This pivotal role will leverage advanced computational techniques to design and optimize novel drug candidates. You will be responsible for developing and implementing state-of-the-art computational methodologies to support drug discovery programs, focusing on areas such as molecular modeling, virtual screening, QSAR, cheminformatics, and molecular dynamics simulations. The ideal candidate will possess a deep understanding of chemical principles and their application in biological systems.

Key responsibilities include designing and executing large-scale virtual screening campaigns, analyzing results, and prioritizing compounds for experimental validation. You will collaborate closely with medicinal chemists, biologists, and pharmacologists to integrate computational findings into ongoing research projects, providing critical insights that drive project progression. Developing novel computational algorithms and workflows to address specific research challenges will be a significant part of your contribution. You will also be responsible for the interpretation and presentation of complex computational data to internal teams and external collaborators. The Principal Scientist will guide the strategic direction of computational chemistry efforts within the organization, mentor junior scientists, and stay current with the latest advancements in the field. A strong publication record in peer-reviewed journals and experience in presenting at scientific conferences are highly desirable. This position offers a unique opportunity to make a significant impact on the development of life-saving therapies in a dynamic and intellectually stimulating environment.

Qualifications:

• Ph.D. in Computational Chemistry, Cheminformatics, Molecular Modeling, or a related field.
• Minimum of 10 years of post-doctoral or industry experience in computational chemistry applied to drug discovery.
• Extensive experience with molecular modeling software (e.g., Schrodinger, MOE, Discovery Studio) and quantum chemistry packages (e.g., Gaussian, ORCA).
• Proficiency in scripting languages (e.g., Python, Perl) for workflow automation and data analysis.
• Demonstrated expertise in virtual screening, QSAR modeling, pharmacophore modeling, and molecular dynamics simulations.
• Strong understanding of medicinal chemistry principles and drug discovery processes.
• Proven ability to lead research projects and mentor junior scientists.
• Excellent problem-solving, analytical, and communication skills.
• Experience with high-performance computing environments.
• Record of impactful publications and presentations in computational chemistry and drug discovery.

Job Description

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.

This role will play a pivotal role in discovering first-best-in-class small molecules, bifunctional degraders, and RNA/oligonucleotides by leveraging computational chemistry and cheminformatics methods to design molecules as well as providing scientific mentoring and leadership to junior members of the team. The person will be tightly integrated into the computational chemistry team and also provide timely and innovative designs and support to our drug discovery programs. Additionally, the role will collaborate closely with global chemistry, structural biology, DMPK, and safety experts for molecular design and help to define a roadmap for computational tools that empower medicinal chemists in their design efforts. While the role will focus on a specific set of programs at any point in time, the drug discovery programs span Takeda's therapeutic areas, including oncology, neuroscience, gastroenterology, and inflammation.

Accountabilities:

• Co-design molecules for several drug discovery programs across various modalities including small molecules, molecular glues, degraders, and RNA/oligonucleotides
• Demonstrate expert understanding of computational chemistry principles and their application within a multidisciplinary drug discovery environment
• Provide crucial technical knowledge and input to project teams to drive decision-making in drug discovery projects by applying in-depth knowledge of structure-activity relationships (SAR), target biology, and predictive methods for assessing on- and off-target activity, physical properties, pharmacokinetics / pharmacodynamics (PK/PD), and synthetic feasibility
• Implement and execute innovative computational methodologies and tools such as AI-based drug discovery, state-of-the-art commercial and open-source software tools/methods
• Mentor junior computational chemists on molecular design best practices
• Open to traveling and spending time on both sites as required
• Serve as a trusted thought partner, helping to drive ideation and execution of innovative chemistry strategies that meet Takeda's therapeutic goals

Education & Competencies (Technical and Behavioral): The ideal candidate will have demonstrated experience impacting drug discovery exemplified by delivering molecules to the clinic, leveraging cutting-edge physics-based modeling, AI/ML-driven approaches, and generative chemistry, collaborating effectively with biologists, structural biologist, pharmacologists, DMPK scientists as well as leading and mentoring computational chemistry teams.

PhD in Computational Chemistry, Chemical Physics, Medicinal Chemistry, or related disciplines, with 20+ years of experience in pharmaceutical or biotech

Deep expertise in structure-based design, ligand-based design, and cheminformatics with a strong background in medicinal chemistry principles

Proven track record in using computational methods to drive small molecule drug discovery, from hit identification to clinical candidate selection

Extensive knowledge of computational chemistry tools, including docking, molecular dynamics, FEP, QSAR modeling, and generative AI

Strong programming and scripting skills (e.g., Python, R, C/C++) with experience in building and automating computational workflows

Strong publication record demonstrating innovative contributions to computational chemistry and drug discovery

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: $208,200.00 - $327,140.00

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.

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 TakedasPrivacy 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

At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.

Objective / Purpose:

This role will play a pivotal role in discovering first-/best-in-class small molecules, bifunctional degraders, and RNA/oligonucleotides by leveraging computational chemistry and cheminformatics methods to design molecules as well as providing scientific mentoring and leadership to junior members of the team. The person will be tightly integrated into the computational chemistry team and also provide timely and innovative designs and support to our drug discovery programs. Additionally, the role will collaborate closely with global chemistry, structural biology, DMPK, and safety experts for molecular design and help to define a roadmap for computational tools that empower medicinal chemists in their design efforts. While the role will focus on a specific set of programs at any point in time, the drug discovery programs span Takedas therapeutic areas, including oncology, neuroscience, gastroenterology, and inflammation.

Accountabilities:

• Co-design molecules for several drug discovery programs across various modalities including small molecules, molecular glues, degraders, and RNA/oligonucleotides
• Demonstrate expert understanding of computational chemistry principles and their application within a multidisciplinary drug discovery environment
• Provide crucial technical knowledge and input to project teams to drive decision-making in drug discovery projects by applying in-depth knowledge of structure-activity relationships (SAR), target biology, and predictive methods for assessing on- and off-target activity, physical properties, pharmacokinetics / pharmacodynamics (PK/PD), and synthetic feasibility
• Implement and execute innovative computational methodologies and tools such as AI-based drug discovery, state-of-the-art commercial and open-source software tools/methods
• Mentor junior computational chemists on molecular design best practices
• Open to traveling and spending time on both sites as required
• Serve as a trusted thought partner, helping to drive ideation and execution of innovative chemistry strategies that meet Takedas therapeutic goals

Education & Competencies (Technical and Behavioral):

The ideal candidate will have demonstrated experience impacting drug discovery exemplified by delivering molecules to the clinic, leveraging cutting-edge physics-based modeling, AI/ML-driven approaches, and generative chemistry, collaborating effectively with biologists, structural biologist, pharmacologists, DMPK scientists as well as leading and mentoring computational chemistry teams.

PhD in Computational Chemistry, Chemical Physics, Medicinal Chemistry, or related disciplines, with 20+ years of experience in pharmaceutical or biotech

Deep expertise in structure-based design, ligand-based design, and cheminformatics with a strong background in medicinal chemistry principles

Proven track record in using computational methods to drive small molecule drug discovery, from hit identification to clinical candidate selection

Extensive knowledge of computational chemistry tools, including docking, molecular dynamics, FEP, QSAR modeling, and generative AI

Strong programming and scripting skills (e.g., Python, R, C/C++) with experience in building and automating computational workflows

Strong publication record demonstrating innovative contributions to computational chemistry and drug discovery

ADDITIONAL INFORMATION:

• The position will be based in Cambridge, MA. This position is currently classified as hybrid by Takedas 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:

$208,200.00 - $327,140.00

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-termincentives. 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

YesIt 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.
#J-18808-Ljbffr

Position Overview:

Neomorph is seeking a highly experienced and strategic Associate Principal Scientist to join our dynamic and collaborative Computational Chemistry team. This individual contributor role is ideal for someone who thrives in a fast-paced startup environment and is eager to shape the future of targeted protein degradation and small molecule drug discovery.

As a senior member of the Computational Chemistry group, you will play a critical role in advancing discovery programs from target assessment through candidate nomination. You'll partner closely with medicinal chemistry, structural biology, biophysics, and biology colleagues to integrate computational strategies into program decision-making. Beyond direct project impact, you will also help drive the evolution of Neomorph's computational capabilities, championing innovation and deploying novel tools and methods.

This is a unique opportunity to contribute scientifically while helping to shape the strategic direction of a growing function at the cutting edge of degrader drug discovery.

Key Responsibilities:

• Serve as a scientific lead and primary computational chemistry contributor on one or more drug discovery programs, guiding design strategies through all phases of the discovery process.
• Integrate structure- and ligand-based design, cheminformatics, and predictive modeling approaches to accelerate hit identification, hit-to-lead, and lead optimization.
• Design and prioritize novel compounds using hypothesis-driven approaches informed by structural data, SAR, molecular modeling, and ML/AI tools.
• Apply and enhance state-of-the-art computational chemistry methodologies, including protein-ligand docking, molecular dynamics (MD), free energy calculations, and ADMET prediction.
• Collaborate cross-functionally to influence program strategy and compound design, bringing both depth and creativity to design hypotheses.
• Explore and evaluate new computational tools, workflows, and platforms to expand and enhance Neomorph's internal capabilities.
• Mentor and provide scientific guidance to less experienced team members across functions; contribute to project team leadership through influence, not direct line management.
• Present findings and strategic recommendations to cross-functional teams and scientific leadership.

Required Qualifications:

• PhD in Computational Chemistry, Theoretical Chemistry, or a related field with 6+ years, MS with 9+ years, or BS with 12+ years of relevant industry experience in drug discovery.
• Demonstrated impact as a lead computational chemist on drug discovery programs, including significant contributions to compound progression and decision-making.
• Deep expertise in structure-based drug design, molecular modeling, and ligand-based approaches, with working knowledge of medicinal chemistry principles.
• Hands-on experience with molecular dynamics simulations (e.g., AMBER, GROMACS, OpenMM) and free energy calculations (e.g., FEP+, TI, MM-GBSA).
• Proficiency in relevant commercial and open-source software suites (e.g., Schrdinger, OpenEye) and fluency in scripting/programming languages (e.g., Python, R).
• Proven ability to integrate complex data and translate computational insights into actionable recommendations.
• Strong communication, collaboration, and problem-solving skills with the ability to influence cross-functional teams and drive strategic discussions.

Preferred Qualifications:

• Experience applying generative AI, machine learning, or advanced cheminformatics techniques to small molecule design.
• Familiarity with targeted protein degradation or protein-protein interaction drug discovery.
• Experience in developing and optimizing cloud-based computational workflows.
• Knowledge of quantum chemistry methods, bioinformatics tools, and/or data integration strategies.

What we offer:

• Industry competitive compensation
• Annual target bonus
• Stock options
• 401K plan
• Career advancement opportunities
• Monthly town halls to share business and scientific updates

Work Hard, Stay Well

• Comprehensive medical, dental, and vision plans for employees and their dependents
• Health and Dependent Care FSA and HSA Plan with monthly Neomorph contribution
• Employee Assistance Program
• 10 holidays + Winter Shutdown + 3 weeks of vacation time with additional accruals after 2nd year of employment, separate sick leave.
• Supplemental pay for Pregnancy Disability Leave
• Paid Parental Leave for employees with a newborn child or a child placed with them for adoption or foster care

Lifestyle

• Casual work environment
• Volunteer days off each year to spend time contributing to causes you care about
• Flexible work schedule
• Access to onsite gym
• Onsite space to store your bicycle (or surfboard)

Have Fun!

We believe in work/life balance and Fun is at the core of our Core Values. In addition to department and company happy hours, we have regular company-wide and department lunches and social events (ie Padres games, summer picnic, holiday party, bring your kids to work day).

About Us:

Neomorph is a venture backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against 'undruggable targets'. Our team is comprised of industry leading experts in protein degradation and molecular glues who have a track record of ground-breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient-first, science-driven approach is complemented by our dedication to a supportive and collaborative work environment.

Neomorph is headquartered in San Diego, California.

Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state or local law.

Notice to agencies: Neomorph will not accept unsolicited assistance from recruiting/search agencies for this employment opportunity. Please, no phone calls or emails. All resumes submitted by recruiting or search agencies to any employee at Neomorph via email, the Internet or in any form and/or method without a valid written search/recruitment agreement in place for this position will be deemed the sole property of Neomorph. No fee will be paid in the event the candidate is hired by Neomorph as a result of the referral or through other means.

**Job Description**
**Position Description**
We are seeking a creative, self-motivated computational chemist with exceptional interpersonal and problem-solving skills to join our Modeling and Informatics (M&I) team.
As part of the Discovery Chemistry family, M&I employs state of the art capabilities in predictive sciences, AI/ML and structure-based drug design to accelerate our invention of transformative therapeutics for patients.
We're expanding our capabilities in peptide computational chemistry to support our ambitious strategy for next-generation therapeutic discovery.
We are seeking a strategic thinker and accomplished computational drug hunter to take on leadership of our peptide modeling capability. This will be a network-facing position, and will be working across geographical and departmental boundaries to advance our computational capabilities for one of our high investment modalities: macrocyclic peptides. This position will carry significant influence on our discovery organization, from target identification through delivery of clinical candidates across our fast-growing peptide project portfolio. With in-house access to the most innovative screening techniques, and world-class medicinal chemistry, this position offers a wealth of opportunities to impact our discovery pipeline and ultimately save and improve patient lives.
**Key responsibilities will include:**
**Scientific Innovation:**
+ Design and optimization of peptide drug candidates using advanced computational techniques as a member of discovery teams
+ Advancing our peptide modeling capabilities through invention of novel computational methodologies as necessary to drive impact
+ Coordinating with adjacent functional teams (e.g. Research IT, Informatics) to implement new methods and workflows to support peptide drug discovery across our organization, including physics-based and AI/ML approaches
+ Functioning as a subject matter champion for ligand- and structure-based drug design across our discovery network
**Building Relationships:**
+ Trusted partner for Discovery Chemistry and adjacent functions for peptides expertise
+ Building fruitful collaborations with stakeholders across medicinal chemistry, pharmacokinetics & pharmacodynamics, quantitative biosciences, and therapeutic area biology
+ Contributing to the continued scientific growth and development of both M&I and Chemistry colleagues as a mentor and influencer both locally and across our network
+ Contributing to the reputation of our Company's peptide capabilities through presentation at conferences and publications, and cultivating relationships with external experts
**Strategy** :
+ Leading specific strategic initiatives to enable our future vision for computational chemistry approaches for drug discovery - with a particular focus on peptides
+ Enabling a design-driven and predict-first culture throughout our Company's Chemistry
+ Contributing to our Company's overarching drug discovery strategy
We recognize that the diversity in our team is our strength and are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a diverse group of scientists to drive our core mission.
**Position Qualifications** **:**
**Education Minimum Requirement:**
+ Ph.D. or M.S. degree in chemistry, biochemistry, biophysics, or equivalent with a computational emphasis.
**Required Experience and Skills:**
+ For Ph.D. holders: 8 years of relevant professional experience beyond graduation (i.e., Pharma, Biotech or equivalent), or 11 years with a M.S. degree.
+ Exceptional oral and written communication skills, with a demonstrated ability to positively and impactfully influence team decisions in drug discovery
+ Ability to communicate, collaborate and deliver results in a fast-paced, global environment and to manage multiple priorities simultaneously
+ Ability to see the ' _big picture_ ', and to identify opportunities for impact now and in the future
+ Expertise in general molecular modeling techniques (docking, molecular simulation, homology modeling, quantum mechanics, QSAR / machine learning, ligand- and structure-based design) with modern software packages (e.g. Schrodinger, OpenEye, CCG)
+ Experience in leading strategic scientific initiatives relevant to drug discovery
+ Skilled in scientific programming (e.g. Python, Pipeline Pilot) and data analytics (e.g. Spotfire) and democratizing coding and workflows
+ Passion for mentoring and coaching scientific peers
**Preferred Experience and Skills:**
+ People management is possible for this position, but it can be tailored to fit the right candidate's preferred development pathway
Current Employees apply HERE ( Contingent Workers apply HERE ( and Puerto Rico Residents Only:**
Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here ( if you need an accommodation during the application or hiring process.
As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:
EEOC Know Your Rights ( GINA Supplement
We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.
Learn more about your rights, including under California, Colorado and other US State Acts ( Hybrid Work Model**
Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as "remote".
The salary range for this role is
$169,700.00 - $267,200.00
This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee's position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.
The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.
We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at .
You can apply for this role through (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.
**San Francisco Residents Only:** We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
**Los Angeles Residents Only:** We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance
**Search Firm Representatives Please Read Carefully**
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.
**Employee Status:**
Regular
**Relocation:**
Domestic
**VISA Sponsorship:**
No
**Travel Requirements:**
10%
**Flexible Work Arrangements:**
Not Applicable
**Shift:**
Not Indicated
**Valid Driving License:**
No
**Hazardous Material(s):**
N/A
**Required Skills:**
Data Science, High Performance Computing (HPC), Machine Learning, Researching, Scientific Modeling
**Preferred Skills:**
**Job Posting End Date:**
08/30/2025
***A job posting is effective until 11:59:59PM on the day** **BEFORE** **the listed job posting end date. Please ensure you apply to a job posting no later than the day** **BEFORE** **the job posting end date.**
**Requisition ID:** R347303

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**
At Takeda, we are a forward-looking, world-class R&D organization that unlocks innovation and delivers transformative therapies to patients. By focusing R&D efforts on three therapeutic areas and other targeted investments, we push the boundaries of what is possible to bring life-changing therapies to patients worldwide.
**_Objective / Purpose:_**
This role will play a pivotal role in discovering first-/best-in-class small molecules, bifunctional degraders, and RNA/oligonucleotides by leveraging computational chemistry and cheminformatics methods to design molecules as well as providing scientific mentoring and leadership to junior members of the team. The person will be tightly integrated into the computational chemistry team and also provide timely and innovative designs and support to our drug discovery programs. Additionally, the role will collaborate closely with global chemistry, structural biology, DMPK, and safety experts for molecular design and help to define a roadmap for computational tools that empower medicinal chemists in their design efforts. While the role will focus on a specific set of programs at any point in time, the drug discovery programs span Takeda's therapeutic areas, including oncology, neuroscience, gastroenterology, and inflammation.
**_Accountabilities:_**
+ Co-design molecules for several drug discovery programs across various modalities including small molecules, molecular glues, degraders, and RNA/oligonucleotides
+ Demonstrate expert understanding of computational chemistry principles and their application within a multidisciplinary drug discovery environment
+ Provide crucial technical knowledge and input to project teams to drive decision-making in drug discovery projects by applying in-depth knowledge of structure-activity relationships (SAR), target biology, and predictive methods for assessing on- and off-target activity, physical properties, pharmacokinetics / pharmacodynamics (PK/PD), and synthetic feasibility
+ Implement and execute innovative computational methodologies and tools such as AI-based drug discovery, state-of-the-art commercial and open-source software tools/methods
+ Mentor junior computational chemists on molecular design best practices
+ Open to traveling and spending time on both sites as required
+ Serve as a trusted thought partner, helping to drive ideation and execution of innovative chemistry strategies that meet Takeda's therapeutic goals
**_Education & Competencies (Technical and Behavioral):_**
The ideal candidate will have demonstrated experience impacting drug discovery exemplified by delivering molecules to the clinic, leveraging cutting-edge physics-based modeling, AI/ML-driven approaches, and generative chemistry, collaborating effectively with biologists, structural biologist, pharmacologists, DMPK scientists as well as leading and mentoring computational chemistry teams.
- PhD in Computational Chemistry, Chemical Physics, Medicinal Chemistry, or related disciplines, with 20+ years of experience in pharmaceutical or biotech
- Deep expertise in structure-based design, ligand-based design, and cheminformatics with a strong background in medicinal chemistry principles
- Proven track record in using computational methods to drive small molecule drug discovery, from hit identification to clinical candidate selection
- Extensive knowledge of computational chemistry tools, including docking, molecular dynamics, FEP, QSAR modeling, and generative AI
- Strong programming and scripting skills (e.g., Python, R, C/C++) with experience in building and automating computational workflows
- Strong publication record demonstrating innovative contributions to computational chemistry and drug discovery
**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:**
$208,200.00 - $327,140.00
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.

**Job Description**
**Position Description**
We are seeking a creative, self-motivated computational chemist with exceptional interpersonal and problem-solving skills to join our Modeling and Informatics (M&I) team.
As part of the Discovery Chemistry family, M&I employs state of the art capabilities in predictive sciences, AI/ML and structure-based drug design to accelerate our invention of transformative therapeutics for patients.
We're expanding our capabilities in peptide computational chemistry to support our ambitious strategy for next-generation therapeutic discovery.
We are seeking a strategic thinker and accomplished computational drug hunter to take on leadership of our peptide modeling capability. This will be a network-facing position, and will be working across geographical and departmental boundaries to advance our computational capabilities for one of our high investment modalities: macrocyclic peptides. This position will carry significant influence on our discovery organization, from target identification through delivery of clinical candidates across our fast-growing peptide project portfolio. With in-house access to the most innovative screening techniques, and world-class medicinal chemistry, this position offers a wealth of opportunities to impact our discovery pipeline and ultimately save and improve patient lives.
**Key responsibilities will include:**
**Scientific Innovation:**
+ Design and optimization of peptide drug candidates using advanced computational techniques as a member of discovery teams
+ Advancing our peptide modeling capabilities through invention of novel computational methodologies as necessary to drive impact
+ Coordinating with adjacent functional teams (e.g. Research IT, Informatics) to implement new methods and workflows to support peptide drug discovery across our organization, including physics-based and AI/ML approaches
+ Functioning as a subject matter champion for ligand- and structure-based drug design across our discovery network
**Building Relationships:**
+ Trusted partner for Discovery Chemistry and adjacent functions for peptides expertise
+ Building fruitful collaborations with stakeholders across medicinal chemistry, pharmacokinetics & pharmacodynamics, quantitative biosciences, and therapeutic area biology
+ Contributing to the continued scientific growth and development of both M&I and Chemistry colleagues as a mentor and influencer both locally and across our network
+ Contributing to the reputation of our Company's peptide capabilities through presentation at conferences and publications, and cultivating relationships with external experts
**Strategy** :
+ Leading specific strategic initiatives to enable our future vision for computational chemistry approaches for drug discovery - with a particular focus on peptides
+ Enabling a design-driven and predict-first culture throughout our Company's Chemistry
+ Contributing to our Company's overarching drug discovery strategy
We recognize that the diversity in our team is our strength and are committed to creating an inclusive environment for all employees. Successful candidates must demonstrate inclusive behaviors in working with a diverse group of scientists to drive our core mission.
**Position Qualifications** **:**
**Education Minimum Requirement:**
+ Ph.D. or M.S. degree in chemistry, biochemistry, biophysics, or equivalent with a computational emphasis.
**Required Experience and Skills:**
+ For Ph.D. holders: 8 years of relevant professional experience beyond graduation (i.e., Pharma, Biotech or equivalent), or 11 years with a M.S. degree.
+ Exceptional oral and written communication skills, with a demonstrated ability to positively and impactfully influence team decisions in drug discovery
+ Ability to communicate, collaborate and deliver results in a fast-paced, global environment and to manage multiple priorities simultaneously
+ Ability to see the ' _big picture_ ', and to identify opportunities for impact now and in the future
+ Expertise in general molecular modeling techniques (docking, molecular simulation, homology modeling, quantum mechanics, QSAR / machine learning, ligand- and structure-based design) with modern software packages (e.g. Schrodinger, OpenEye, CCG)
+ Experience in leading strategic scientific initiatives relevant to drug discovery
+ Skilled in scientific programming (e.g. Python, Pipeline Pilot) and data analytics (e.g. Spotfire) and democratizing coding and workflows
+ Passion for mentoring and coaching scientific peers
**Preferred Experience and Skills:**
+ People management is possible for this position, but it can be tailored to fit the right candidate's preferred development pathway
Current Employees apply HERE ( Contingent Workers apply HERE ( and Puerto Rico Residents Only:**
Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here ( if you need an accommodation during the application or hiring process.
As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics. As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:
EEOC Know Your Rights ( GINA Supplement
We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.
Learn more about your rights, including under California, Colorado and other US State Acts ( Hybrid Work Model**
Effective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as "remote".
The salary range for this role is
$169,700.00 - $267,200.00
This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee's position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.
The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.
We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at .
You can apply for this role through (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.
**San Francisco Residents Only:** We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance
**Los Angeles Residents Only:** We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance
**Search Firm Representatives Please Read Carefully**
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.
**Employee Status:**
Regular
**Relocation:**
Domestic
**VISA Sponsorship:**
No
**Travel Requirements:**
10%
**Flexible Work Arrangements:**
Not Applicable
**Shift:**
Not Indicated
**Valid Driving License:**
No
**Hazardous Material(s):**
N/A
**Required Skills:**
Data Science, High Performance Computing (HPC), Machine Learning, Researching, Scientific Modeling
**Preferred Skills:**
**Job Posting End Date:**
08/30/2025
***A job posting is effective until 11:59:59PM on the day** **BEFORE** **the listed job posting end date. Please ensure you apply to a job posting no later than the day** **BEFORE** **the job posting end date.**
**Requisition ID:** R347303

Our client, a world-renowned research institution specializing in advanced materials science, is seeking a highly skilled Senior Research Scientist in Computational Chemistry. This pivotal role will involve leveraging cutting-edge computational techniques to design and predict the properties of novel materials for various high-impact applications. The ideal candidate will possess a Ph.D. in Chemistry or a related field, extensive experience with quantum mechanical calculations and molecular dynamics simulations, and a strong publication record. You will be at the forefront of scientific discovery, driving innovation through theoretical and computational approaches.

Key Responsibilities:

• Design and conduct advanced computational chemistry studies using state-of-the-art software and methodologies.
• Develop and refine theoretical models to predict material properties, reaction pathways, and electronic structures.
• Perform quantum mechanical calculations (e.g., DFT, ab initio methods) and molecular dynamics simulations.
• Analyze and interpret complex simulation data, extracting meaningful scientific insights.
• Collaborate with experimental scientists to validate computational predictions and guide material synthesis efforts.
• Contribute to the development of new computational algorithms and workflows.
• Write high-quality scientific manuscripts for peer-reviewed publications and present findings at international conferences.
• Mentor junior researchers and postdoctoral fellows in computational chemistry techniques.
• Manage research projects, including resource allocation and timeline adherence.
• Contribute to grant writing and securing external funding for research initiatives.

Qualifications:

• Ph.D. in Computational Chemistry, Physical Chemistry, Theoretical Chemistry, or a closely related field.
• Minimum of 7 years of postdoctoral and/or industry research experience in computational chemistry.
• Expertise in various computational chemistry software packages (e.g., Gaussian, VASP, LAMMPS, AMBER, NWChem).
• Proven proficiency in scripting languages (e.g., Python, Bash) for workflow automation and data analysis.
• Strong understanding of quantum mechanics, statistical mechanics, and solid-state physics.
• Excellent analytical, problem-solving, and critical thinking skills.
• Exceptional scientific writing and oral communication skills.
• Demonstrated ability to lead research projects and collaborate effectively in a multidisciplinary team.
• Experience with high-performance computing (HPC) environments is essential.
• A strong publication record in leading peer-reviewed journals is required.

This exciting research opportunity is located in Houston, Texas, US . If you are a passionate and accomplished computational chemist looking to push the boundaries of scientific knowledge, we encourage you to apply.