Software Engineer - Biomolecular Structure Software

About Astera

Astera is a private foundation on a mission to steer science and technology toward a better future. We believe the coming years will bring an era of unprecedented scientific and technological advancement as exponential progress in AI converges with central advances in other fields to accelerate innovation. This inflection point provides an unparalleled opportunity to fundamentally rethink the institutions, systems, and tools that drive progress. We have committed a $3.5B endowment to that work and fit the form of our support to the function it serves: grants, investments, and in-house research programs. We accept meaningful risk in the research we back and expect some of it to fail because transformative ideas are rarely the ones already proven. Our projects, and the foundation itself, operate like high-velocity startups, with a high performance bar and competitive compensation to match. We are searching for leaders who are compelled by the challenge of driving high-impact change in the way science is funded, conducted, and communicated. You can read more about our mission, vision, and programming at astera.org/vision.

Team Overview

Prism is making protein motion measurable, predictable, and actionable. Proteins are always moving, and that movement drives their function: binding, catalysis, allostery, selectivity, and mutational effects all emerge from conformational ensembles, the distribution of states a protein moves between. Yet most structural data rests on static snapshots that capture form, not function, because motion has been hard to measure and interpret. That has left us without critical levers to correct proteins in disease or engineer them for new purposes. We are building a team of structural biologists, computational scientists, and engineers to develop open tools, methods, and infrastructure for studying protein dynamics from experimental data. By combining experimental measurement, ensemble modeling, and machine learning, we aim to move structural biology from describing what proteins look like to predicting how they behave.

Prism sits within Radial, Astera's life sciences division (https://astera.org/radial/).

Position Summary

The Astera Institute’s Prism project seeks a full-time on-site software engineer to lead design and development of new software tools for working with biomolecular structures and experimental data used for biomolecular structure determination in a machine-learning friendly way. The successful candidate will be involved in API design, architecture, and implementation of the package, as well as refactoring existing software to use the new tools. This position reports to the Machine Learning Team Lead.

This is a full-time position.

Responsibilities

• Reviewing existing APIs and codebases to identify constraints and needs

• Reviewing existing requirements and translating them into a final API, and building consensus both within Prism and externally around that API

• Working with scientists to define requirements.

• Working with Prism and external scientists to identify where existing software libraries can be used and what must be built new.

• Working with Prism and external scientists to ensure correctness of any calculations performed on structures and data.

• Writing Python code to implement software, and possibly C/C++ libraries as needed for high performance, including GPU kernels written with CUDA

Qualifications and Experience

• Bachelor’s degree in Computer Science or related field with at least 5 years of work experience.

• Experience building new software packages from the ground up.

• A track record of building software for critical scientific applications.

• Experience collaborating with scientists from diverse backgrounds.

• Experience working with machine learning pipelines, data preparation, etc. (experience training ML models is not required).

• Nice to have: experience with structural biology data.

Cultural Alignment

• Surprising problem-solver – you love finding unexpected solutions to problems we don't even know we have, and see options where others only see constraints.

• Flexible by default – you don't draw hard lines around your job description and expect requirements to evolve.

• Bias to action – when in doubt, you build and test an idea.

• High standards, internally driven – you don’t settle for the first thing that seems to work, you come up with new ways to break it to make sure it is correct.

• Open to feedback – you create opportunities to give and receive honest feedback, staying focused on both personal and team growth.

• Operate with the highest levels of integrity, judgment, and stewardship — you treat peers, collaborators, and vendors with genuine respect for their time and contributions.

• Embrace the tools that define great work today – Astera is building for an AI-driven future and equips the team accordingly.

Location

This position is on-site at our Emeryville, CA location. Some travel (10%) may be required from time-to-time for in-person collaboration and work.

Compensation

This role's pay range is $240,000 – $280,000 per year, based on experience, skills, and location.

Benefits

Benefits include:

• Top tier health insurance plans with 99% of premiums covered by Astera for employees and dependents

• Daily lunch that brings the full office together, plus a well-stocked fridge and pantry

• Licenses for frontier AI tools and software

• 403(b) retirement plans, flexible paid time off, paid parental leave, commuter benefits, and health and dependent care FSAs

Equal Opportunity Employment & Accommodations

Astera Institute is an equal opportunity employer and is invested in fostering a culture where everyone can thrive. We are committed to equity and inclusion, and we encourage women, people of color, LGBTQIA individuals, people with disabilities, members of ethnic minorities, foreign-born residents, older members of society, and others from minority communities and diverse backgrounds to apply.

Astera Institute is committed to providing reasonable accommodations for qualified individuals with disabilities in the job application and interview process. If you need an accommodation, please contact us at [email protected] and we will work with you to meet your needs.