About the role

As a computational chemist at Treeline, you will play a key role in the application of in silico methodology to the design of small molecule oncology therapeutics. You will collaborate with medicinal chemists, structural biologists, biophysicists, other computational chemists and data scientists to drive good decision-making and smart risk-taking in all areas of drug discovery, including but not limited to cryptic pocket identification, druggability assessment, hit identification, and multivariate molecular profile optimization. Additionally, you will drive advances in technology and infrastructure through internal and external engagement to build a world-class computational chemistry platform that accelerates the path to medicines.


Watertown, MA; San Diego, CA.


  • Collaborate with multi-disciplinary teams in the design of medicines using protein structure-based and ligand-based approaches involving physics, machine learning and other disciplines.
  • In partnership with other computational and medicinal chemists, design molecules to optimize ADMET, physicochemical properties, selectivity, and potency.
  • Collaborate with biologists, medicinal chemists, and data scientists to develop testable hypotheses, design experiments, and analyze the output of both experimental and virtual screens for hit identification.
  • Ensure rigorous model validation.
  • Survey the literature for novel computational chemistry methodology and algorithms, and introduce to the broader team when appropriate.
  • Work collaboratively with the Treeline team to apply and enhance computational infrastructure needed to drive our projects forward.


  • PhD or equivalent in Computational Chemistry, Cheminformatics, or related quantitative fields with 2+ years post-PhD experience in the Pharmaceutical/Biotechnology Industry (or MS in one of these fields with 7+ years of related experience).
  • Strong scientific understanding of chemistry, retrosynthetic design, biological assays, drug metabolism, pharmacokinetics, pharmacodynamics, and toxicology, and a strong understanding of basic statistics.
  • Track record of directly impacting the discovery of high quality hits, leads, and clinical assets using computational design approaches.
  • Strong scientific curiosity and ability to dig deeply through various data types to gain insights and develop testable hypotheses.
  • Extensive experience evaluating, developing and impactfully applying computational methodologies to drive decision-making and smart risk-taking in drug discovery.
  • Extensive hands-on experience applying any of the following approaches to drug discovery: docking and scoring, virtual screening, molecular dynamics, homology modeling, QSAR modeling, PBPK and PK/PD modeling, quantum chemistry.
  • Hands on experience with cheminformatics, data aggregation, manipulation, integration, mining, and analysis.
  • Experience with a small molecule chemistry toolkits: DeepChem, RDKit, OEChem, etc.
  • Experience with machine learning techniques such as reinforcement learning, meta learning, active learning, generative models, regression models, binary classifiers, including application to medicinal chemistry problems.
  • Extensive experience working in command line interfaces and fluency in scripting programming languages e.g., scientific Python (numpy, scipy, scikit-learn).
  • Proficient in data visualization.
  • Proven ability to influence across multi-disciplinary teams and interact with external experts in academic institutions as well as CROs.
  • Excellent written and oral communication skills, including an ability to explain complex ideas to computational scientists, experimentalists, and clinicians.
  • Capable of establishing strong working relationships across the organization to define and solve problems that will benefit the whole.
  • Ability to manage multiple projects simultaneously and flexibly manage priorities.

Notice to Search Firms/Third-Party Recruitment Agencies (Recruiters)

The Human Resources team manages the recruitment and employment process for Treeline Biosciences. To protect the interests of all parties involved, Treeline Biosciences will only accept resumes from a recruiter if an executed search agreement directed to the particular position or positions is in place at the start of the recruitment effort. Unsolicited resumes sent to Treeline Biosciences from recruiters do not constitute any type of relationship between the recruiter and Treeline Biosciences and do not obligate Treeline Biosciences in any way to pay fees should we hire from those resumes. Recruiters are requested not to contact or present candidates directly to our hiring manager or employees.

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