Senior Scientist, Structural Data Representation

Astera Institute; Emeryville (CA); On-site; USD 220,000 - 260,000; Full time

Benefits offered by this job

Health insurance

Daily lunch

AI tool licenses

403(b) plan

Flexible PTO

Visa sponsorship

Job summary

Astera Institute in Emeryville, CA seeks a Senior Scientist, Structural Data Representation to lead encoding of conformational ensembles and connect them to visualization, ML, and computational pipelines. You will head a small Prism team and collaborate with external developers to standardize ensemble data for the field.

You will design encoding models, build databases, support native integration with open-source structural biology tools, and partner with PDB and others to advance public-good

Qualifications

• PhD in a relevant area; at least 4 years of work experience.
• Experience managing a team of scientists or engineers.
• Deep understanding of how structural models are encoded and used for interpretation, including fluency in mmCIF and its extension mechanisms.
• Strong coding experience, with a track record of writing software that other people use.
• Clear communication across technical communities; can explain data standards to structural biologists, ML researchers, and software developers.
• Execution-forward approach; ships working versions, gathers feedback, and iterates.
• Nice to have: product development experience.
• Nice to have: experience building scientific databases or visualization tools.

Responsibilities

• Lead and mentor a team of 2-3 scientists and software engineers, setting priorities and maintaining execution as ensemble models move to broad adoption.
• Work with the Scientific Program Director to determine strategy and prioritization of approaches and science within your team.
• Partner with Prism's modeling and ensemble-functional team to ensure cohesion and data representation supports downstream analyses.
• Design, test, and deploy encoding models and schemas for conformational ensembles.
• Direct the development of databases to connect dynamic ensemble models for data sharing and downstream use, including visualization tools.
• Collaborate with external partners such as the PDB and tool developers to bridge Prism with external work.
• Partner with teams behind open-source tools to implement native support for ensemble models.

Skills

Team management

mmCIF proficiency

Software development

Cross-community communication

Execution mindset

Education

PhD in a relevant area

Job description

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.

About Prism:

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. As a result, we lack critical levers to correct proteins in disease and engineer them for new purposes. Prism is building open, usable tools, methods, and infrastructure to study protein dynamics from experimental data, and applying them to pressing biological questions, including binding affinity, enzyme engineering, and explaining pathogenic variants. Prism sits with Radial, Astera's Life Sciences Division.

About Radial:

Radial is Astera's life sciences division. We tackle foundational problems in biology while simultaneously prototyping better ways to fund, organize, and share research. Radial builds programs in-house, funds external teams, and designs partnerships in service of public-good science.

Position Summary:

Prism is seeking a full-time Senior Scientist, Structural Data Representation to lead how Prism's conformational ensemble models are encoded, organized into databases, and connected to the tools the rest of the field uses. This includes visualization, machine learning models, and other computational pipelines. You will lead a small Prism team and partner with external developer communities to make ensemble data a standard part of structural biology. This position reports to the Scientific Program Director.

Responsibilities:

• Lead and mentor a team of 2-3 scientists and software engineers, setting priorities and keeping execution moving as you take Prism's ensemble models from internal research to broad adoption across the field.

• Work with the Scientific Program Director to determine strategy and prioritization of approaches and science within your team.

• Partner with Prism's modeling and ensemble-functional team, alongside the Scientific Program Director, to ensure cohesion across the project, including making sure data representation choices serve both what models produce and what downstream functional analyses need.

• Design, test, and deploy encoding models and schemas for conformational ensembles.

• Direct the development of databases to connect dynamic ensemble models for data sharing and downstream use, including visualization tools.

• Work with external partners such as the PDB and tool developers in the visualization, ML, and computational chemistry space in order to build bridges between work within Prism and external partners.

• Partner with the teams behind widely used open-source structural biology tools to define and implement native support for ensemble models

Qualifications:

• PhD in a relevant area; at least 4 years of work experience

• Experience managing a team of scientists or engineers.

• Deep understanding of how structural models are encoded and used for interpretation, including fluency in mmCIF and its extension mechanisms.

• Strong coding experience, with a track record of writing software that other people use.

• Clear communication across technical communities. You can explain data standards to structural biologists, ML researchers, and software developers, and build agreement among them.

• An execution-forward approach. You ship working versions, gather feedback, and iterate.

• Nice to have: product development experience.

• Nice to have: experience building scientific databases or visualization tools.

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 your role to evolve significantly over 6-12 months.

• Bias to action – you launch and iterate on thoughtful experiments rather than waiting for perfect plans, and you're energized by novel problems.

• High standards, internally driven – you believe you can build the world's best vehicle for unleashing extraordinary individuals to create public goods.

• 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%) will be required for in-person collaboration and presentations. Relocation packages will be considered.

Compensation:

This role's pay range is $220k - $260k per year, based on experience, skills, and location.

Benefits:

• Top-tier health insurance plans with 99% of premiums covered by Astera Institute 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

• Visa Sponsorship

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 [e-mail], and we will work with you to meet your needs.