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Job Information

Merck Scientific Director, Cheminformatics AI/ML in Cambridge, Massachusetts

Job Description

We are seeking an experienced and skilled Cheminformatician and AIML data scientist to join the Cheminformatics group within Modeling and Informatics (M&I) at our Boston/Cambridge, MA or Rahway, NJ sites. This role requires exceptional interpersonal and problem-solving skills, as well as the ability to translate scientific needs into actionable plans for implementing data workflows and infrastructure that accelerate the decision-making process from hit identification to clinical candidate delivery across different therapeutic areas and modalities at our company.

M&I is a diverse and inclusive team within the our Research Laboratories Discovery Chemistry organization, comprising approximately 60 computational chemists, cheminformaticians, and data scientists. We leverage cutting-edge capabilities in structure-based modeling, predictive science, and AI/ML to drive drug design and development globally, with a proven track record of pipeline impact. The selected candidate will work closely with the M&I team and world-class chemistry teams on innovative science that has a wealth of opportunities to impact drug discovery and ultimately save and improve patient lives.

Key responsibilities will include:

Scientific Innovation:

  • Lead the development and implementation of effective AI/ML and cheminformatics workflows to impact all aspects of the Design, Make, Test, and Analyze (DMTA) cycles, including compound idea generation, library design, synthesis planning, and data analysis.

  • Drive and deliver optimized informatics algorithms and workflows to expedite drug discovery pipelines for a broad portfolio of modalities, such as peptides, antibody-drug conjugates, and targeted protein degraders.

  • Initiate and apply novel ML, statistics, and cheminformatics techniques to improve hit identification and hit-to-lead processes for different screening technologies (mRNA display, DNA-Encoded Libraries, high-throughput screening, virtual screening).

  • Identify opportunities, and collaborate with research scientists, IT specialists, and data scientists to find creative cheminformatics solutions to data, workflow, infrastructure, analysis, and modeling challenges.

  • Effectively communicate scientific results internally and externally through presentations and publications.

  • Provide scientific mentoring and training to maximize team impact on pipeline and capability deliverables.

Leadership and management:

  • Manage 12 cheminformaticians and data scientists, fostering talent growth and career development for all direct reports.

  • Foster cross-functional collaborations with stakeholders in discovery chemistry, pharmacokinetics & pharmacodynamics, quantitative biosciences, therapeutic area biology, and information technology.

  • Identify and evaluate new cheminformatics and AI/ML technology and software from commercial sources, open innovation, or external collaborations, strategically incorporating vendor solutions to enable efficient data-driven drug discovery.

  • Promote a data-fluent culture that emphasizes the value of FAIR data and robust, generalizable computational pipelines.

  • Lead aspects of capability builds and working groups while participating in cross-functional matrix teams to advance computational drug discovery at our company.

Position Qualifications :

Education Minimum Requirement:

Ph.D. in cheminformatics, computational chemistry, chemistry, chemical engineering, or related fields

Required Experience and Skills:

  • 7+ years of experience applying cheminformatics and AI/ML approaches to problem-solving in drug discovery, including data mining, method implementation, and workflow automation.

  • Comprehensive knowledge of drug discovery and medicinal chemistry, with the ability to effectively communicate with collaborative scientists from diverse backgrounds.

  • Broad understanding of modern data science methods, particularly machine learning, in advancing drug discovery (e.g., predictive modeling, generative modeling, retrosynthesis prediction, active learning, explainable ML).

  • Excellent oral and written communication skills, with the ability to positively influence team decisions.

  • Strong problem-solving skills with meticulous attention to detail.

  • Proficiency in scripting (Python and/or R), SQL, and cheminformatics toolkits (OEChem, RDKit, DeepChem) with practical application of these skills.

  • Expertise in machine learning libraries (TensorFlow, Keras, PyTorch, Pandas, Scikit-Learn).

  • Familiarity with workflow applications and data analytics software (Pipeline Pilot, Knime, Spotfire).

Preferred Experience and Skills:

  • Expertise in data analysis and modeling in fields such as high-throughput experimentation, DNA-encoded libraries, mRNA display screening, virtual screening, screening hit identification, lead optimization, modality drug design.

  • Experience with IT infrastructure such as database systems, cloud computing (such as Databricks, AWS), and high-performance computing in Linux environments.

  • Experience leading scientific initiatives or capability builds in a matrixed environment relevant to drug discovery.

  • Leadership and people management experience.

  • Track record of scientific publications in peer-reviewed journals.


In accordance with Managers' Policy - Job Posting and Employee Placement, all employees subject to this policy are required to have a minimum of twelve (12) months of service in current position prior to applying for open positions.

If you have been offered a separation benefits package, but have not yet reached your separation date and are offered a position within the salary and geographical parameters as set forth in the Summary Plan Description (SPD) of your separation package, then you are no longer eligible for your separation benefits package. To discuss in more detail, please contact your HRBP or Talent Acquisition Advisor.


Employees working in roles that the Company determines require routine collaboration with external stakeholders, such as customer-facing commercial, or research-based roles, will be expected to comply not only with Company policy but also with policies established by such external stakeholders (for example, a requirement to be vaccinated against COVID-19 in order to access a facility or meet with stakeholders). Please understand that, as permitted by applicable law, if you have not been vaccinated against COVID-19 and an essential function of your job is to call on external stakeholders who require vaccination to enter their premises or engage in face-to-face meetings, then your employment may pose an undue burden to business operations, in which case you may not be offered employment, or your employment could be terminated. Please also note that, where permitted by applicable law, the Company reserves the right to require COVID-19 vaccinations for positions, such as in Global Employee Health, where the Company determines in its discretion that the nature of the role presents an increased risk of disease transmission.

Current Employees apply HERE (https://wd5.myworkday.com/msd/d/task/1422$6687.htmld)

Current Contingent Workers apply HERE (https://wd5.myworkday.com/msd/d/task/1422$4020.htmld)

US 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 (https://survey.sogosurvey.com/r/aCdfqL) if you need an accommodation during the application or hiring process.

We are an Equal Opportunity Employer, committed to fostering an inclusive and diverse workplace. All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status, or other applicable legally protected characteristics. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

EEOC Know Your Rights (https://www.eeoc.gov/sites/default/files/2022-10/22-088_EEOC_KnowYourRights_10_20.pdf)

EEOC GINA Supplement​

Pay Transparency Nondiscrimination (https://www.dol.gov/sites/dolgov/files/OFCCP/pdf/pay-transp_%20English_formattedESQA508c.pdf)

We are proud to be a company that embraces the value of bringing diverse, talented, and committed people together. The fastest way to breakthrough innovation is when diverse ideas 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 (https://www.msdprivacy.com/us/en/CCPA-notice/)

U.S. 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, generally Tuesday, Wednesday and either Monday or 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”.

Under New York State, Colorado State, Washington State, and California State law, the Company is required to provide a reasonable estimate of the salary range for this job. Final determinations with respect to salary will take into account a number of factors, which may include, but not be limited to the primary work location and the chosen candidate’s relevant skills, experience, and education.

Expected salary range:

$184,800.00 - $290,900.00

Available benefits include bonus eligibility, long term incentive if applicable, health care and other insurance benefits (for employee and family), retirement benefits, paid holidays, vacation, and sick days. A summary of benefits is listed here (https://www.benefitsatmerck.com/) .

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:



VISA Sponsorship:

Travel Requirements:

Flexible Work Arrangements:

Not Applicable


Valid Driving License:

Hazardous Material(s):

Required Skills:

Preferred Skills:

Job Posting End Date:


*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.

Job Posting End Date: 07/27/2024

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: R301019