About Generate Biomedicines

Generate Biomedicines is a new kind of therapeutics company – existing at the intersection of machine learning, biological engineering, and medicine – pioneering Generative Biology™ to create breakthrough medicines where novel therapeutics are computationally generated, instead of being discovered. Generate has built a machine learning-powered biomedicines platform with the potential to generate new drugs across a wide range of biologic modalities. This platform represents a potentially fundamental shift in what is possible in the field of biotherapeutic development.

We pursue this audacious vision because we believe in the unique and revolutionary power of generative biology to radically transform the lives of billions, with an outsized opportunity for patients in need. We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Generate was founded in 2018 by Flagship Pioneering and has received over $420 million in funding, providing the resources to rapidly scale the organization. The Company has offices in Somerville and Andover, Massachusetts with over 250 employees.

The Role:

We are seeking a structural biologist with experience developing computational methods for single-particle electron cryo-microscopy (CryoEM) to join our Computational Structure Determination (CSD) team. They will collaborate with our machine learning (ML) and CryoEM teams inventing tools to accelerate and scale structure determination and maximize the impact of the structures we solve.

At Generate, we aim to change the paradigm of structural biology in drug discovery by leveraging single-particle CryoEM as a first-line approach to directly visualize biological molecules throughout the design process. These structures will be directly utilized by our data-driven ML models to reliably program biological function into molecules with precision. This will only be achievable if we can radically increase the scale at which high-resolution structures can be solved with CryoEM.

Towards this goal, the Computational Structure Determination (CSD) team is building out robust, automated computational pipelines that span the entire CryoEM workflow, including specimen preparation, image processing, model building, and structure interpretation. The prospective candidate will be fully empowered to shape and implement this vision as a member of a dynamic and creative team. The candidate will also contribute directly to solving structures with scientists on the CryoEM team, tightly coupling experiment and computation. We are especially interested in candidates with expertise in automated building of molecular models from volumetric CryoEM data and designing computational tools for validating and analyzing these models with minimal human intervention.

Here's how you will contribute:

• Implement and establish best practices for using existing CryoEM tools, especially towards scalable, robust, automated pipelines for determining atomic structures from CryoEM data.
• Contribute to the development of new methodologies (including ML-based ones) for determining and interpreting structural data alongside relevant teams at Generate.
• Work with internal stakeholders to get the most value out of our structural data, especially by designing systems for quantitative analysis, interpretation, and presentation of structures.
• Present scientific results to program teams, external conferences, and executive leadership

The Ideal Candidate will have:

• A PhD in molecular biology, biophysics, biochemistry, computer science, or a related discipline with an emphasis on structural biology and cryo-EM
• Practical expertise determining CryoEM structures from raw EM data using a modern CryoEM software suite (cryoSPARC, cisTEM, or RELION), model-building package (phenix or Rosetta), and molecular visualization software (ChimeraX or molstar).
• Scientific publications demonstrating innovative methods in structural biology
• Proficiency with scientific programming in python, demonstrated in published code
• Excellent communication skills and the ability to work well in a highly collaborative environment

The ideal candidate would also have:

• Foundational knowledge about macromolecular structure, function, and evolution, particularly the thermodynamics of protein folding, binding, and conformational change.
• Confidence with the algorithms underlying modern CryoEM and macromolecular modeling tools, including those from image processing, statistical inference, gradient-based optimization, molecular dynamics simulations, or computational 3D geometry.
• 'Hands on' experimental CryoEM expertise, including preparing specimens and collecting data.
• Experience quantitatively analyzing protein structural data, for example by performing and analyzing simulations with molecular dynamics, Rosetta, or ML-based protein analysis tools
• Experience in developing machine learning methods, especially using deep learning or probabilistic generative models of proteins or scientific imaging data.
• Ability to write robust and performant GPU-accelerated scientific code.
• Experience with workflow managers for ML or scientific computational pipelines (MLFlow, Snakemake, Prefect, or others)

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Generate Biomedicines is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

COVID Safety:

Generate Biomedicines enforces a mandatory vaccination policy for COVID-19. All employees must be fully vaccinated and have received a booster. The purpose of this policy is to safeguard the health of our employees, their families, and the community at large from infectious disease that may be reduced by vaccinations. The company will make exceptions to this policy if required by applicable law and will consider requests for an exemption from this policy due to a medical reason, or because of a sincerely held religious belief, or any other exemptions that may be recognized by applicable.

Recruitment & Staffing Agencies: Generate Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate Biomedicines or its employees is strictly prohibited unless contacted directly by Generate Biomedicines's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate Biomedicines, and Generate will not owe any referral or other fees with respect thereto.