Company Summary:

Founded by Flagship Pioneering in 2021, Metaphore aims to unlock breakthroughs that outperform today’s drugs for maximum patient impact, We adapted this idea to drug discovery. MIMIC™, our computationally driven bioplatform that couples machine learning with molecular mimicry, engineers therapeutics to trigger a desired biological response. Our MIMIC platform opens the possibility to develop engineered medicines with specific features to access a range of targets, including those that were previously intractable. Flagship and Metaphore have also just announced a $600M research collaboration with Novo Nordisk to develop up to two next-generation therapeutics for obesity management.

Metaphore Biotechnologies is a product of Flagship Pioneering’s venture creation engine, which has also given rise to companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally on Fortune’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies.

Position Summary:

Metaphore Biotechnologies is seeking an enthusiastic Computational Protein Design and Machine Learning Scientist to join our computation-guided therapeutic discovery and development engine. In this role, you will work at the interface of physics-based and machine learning-based protein design to develop and deploy state-of-the-art approaches to challenging therapeutic biomolecule discovery and optimization goals. As a member of the modeling team, you will have the opportunity to be a key contributor on a variety of tasks, including de novo design, multi-parameter optimization, inverse folding, sequence-structure-function modeling and more.  You will work closely with Metaphore’s preclinical and platform teams to both develop molecules and delineate the ideal training and validation data for method development.  The ideal candidate will bring experience in molecular modeling of proteins and protein complexes, structure-based design tools, and state-of-the-art deep learning approaches, helping us unlock the potential of molecular mimicry for therapeutics development. This individual will have the opportunity to join a dynamic interdisciplinary team and also be part of the Flagship ecosystem of companies, providing unique networking benefits through regular meetups, collaboration, and an environment of development and discussion around new ideas shaping the fields of computational biology, ML/AI and data-driven drug discovery.

Key Responsibilities:

• Design, implement and evaluate methodologies for structure-based protein design.
• Collaborate with pre-clinical team to design and optimize molecules to achieve therapeutic program aims.
• Collaborate with platform scientists to define and generate training and validation data for optimal method development.
• Maintain up to date on state-of-the-art macromolecular modeling and ML advances.

Qualifications:

• Ph.D. in Computational Biology, Bioengineering, Computer Science or a related field. Post-graduate experience is a plus. 
• Experience with macromolecular modeling, docking and protein design. Experience with Rosetta is highly preferred.  Experience in Molecular Dynamics is a plus.
• Experience with modeling and design of antibodies or antibody-like molecules.
• Experience with state-of-the-art protein design deep learning tools, such as AlphaFold2, RoseTTAFold, RFdiffusion, etc.
• Experience developing machine learning models in the context of protein design or protein property prediction.
• Familiarity with modern deep learning architectures such as Diffusion models, Transformers, Graph Neural Networks, Flow-based models, etc.
• Mastery of python and pytorch.
• Experience with git, docker, cloud computing, and software development best practices.  Experience with ML experiment tracking, model registries and workflow orchestration tools such as Nextflow is a plus.
• Excellent communication, organizational and problem-solving skills.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.