Software Engineer, Computational Chemistry, Atomwise, San Francisco (8 March 2022)

At Atomwise, we invented the first deep learning neural networks for structure-based small molecule drug discovery, and we’re currently deploying it in one of the largest applications of machine learning for life sciences. We work on Alzheimer’s, cancer, diabetes, drug-resistant antibiotics, and other diseases. We’ve partnered with 4 of the top-10 US pharma companies, raised over $100M from top VCs, and have 100+ diverse projects currently running.

To date, Atomwise has raised over $174 million from leading venture capital firms to advance its mission to make better medicines, faster.

Our team has over 50 Ph.D. scientists who contribute to a collaborative academic-like culture that fosters robust scientific and technical discussion. We strongly believe that data wins over opinions, and aim for as little dogma as possible in our decision-making. Our team members have expertise in a wide range of disciplines–from computational chemistry and structural biology to cloud-native best practices–and we regularly have internal seminars open to anyone interested in learning about these topics.

Role Summary

Atomwise uses AI to develop hard-to-target drugs. We are developing novel methods and algorithms for drug discovery that involves building large-scale, distributed, and computationally intensive workloads. This role will tackle the following classes of problems 1) Data has grown exponentially, how do we improve the algorithms, data structures, and databases to handle the increased volume and varying use cases 2) How do we proveably maintain diversity in compounds that are being predicted 3) How can we reduce the cycle time of H2L and LO processes 4) How do we improve active learning infrastructure at Atomwise 5) How to improve our computation infrastructure to handle all the above.

We are leaders in AI-based drug discovery and are at the forefront of such challenges.

Required Qualifications

  • Expert level software engineering skills with Python.
  • Working knowledge of Docker and Kubernetes.
  • Experience developing distributed algorithms and applications on modern cloud platforms.
  • Background requirements:
    • Masters or PhD in computational science (computational chemistry, physics, cheminformatics) + 3-5 years software engineering industry experience OR
    • Bachelors in computer science with 5-7 years of software development experience with a significant amount in biotech software engineering
  • Good communication skills; the ability to work with colleagues of various backgrounds and domain expertise is required.
  • Being able to work with scientists with expertise in medicinal chemistry, cheminformatics and ML is required

Preferred Qualifications

  • Experience developing drug discovery algorithms is highly desired.  For example: vHTS, lead optimization, FEP, ADMET, ultra-large molecular libraries.
  • Knowledge of tools and techniques employed for AI especially in deep learning is highly desired. Experience deploying ML applications and models
  • An advanced degree in chemistry, biochemistry, or similar is highly desired.
  • Experience developing with or contributing to cheminformatics or computational chemistry toolkit or package is highly desired

Compensation & benefits

  • Competitive salary, commensurate with experience
  • Stock compensation plan – you’ll be an Atomwise co-owner
  • Platinum health, dental, and vision benefits
  • 401k with 4% match
  • Funding for professional development and conference attendance.
  • Flexible work schedule
  • Generous parental leave
  • Strong emphasis on collaborative learning and career development

Atomwise is an equal opportunity employer and strives to foster an inclusive workplace. Our mission is to develop better medicines faster, and we know that we need a diverse team to develop medicines that serve diverse populations. Accordingly, Atomwise does not make any employment decisions (including but not limited to, hiring, compensation, and promotions) on the basis of race, religion, color, national origin, gender, gender identity, sexual orientation, age, veteran status, disability status, or any other characteristics protected by applicable federal, state, and local law.

We strongly encourage people of diverse backgrounds and perspectives to apply. Authorization to work in the U.S is required. Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with arrest and conviction records.

Application instructions can be found at this LINK.

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