Computational Protein Engineer

AeroVironment, Inc.; Upper Valley Trailer Court (OH); On-site; USD 140,000 - 190,000; Full time

Benefits offered by this job

Medical benefits

Dental & Vision

401(k) with company matching

9/80 work schedule

Paid holiday shutdown

Job summary

AeroVironment, Inc. in California seeks a Computational Protein Engineer to lead de novo design and optimization of proteins for novel metal separation technologies.

You will use generative design software, machine learning on large datasets, and HPC workflows to advance performance and ownership within a collaborative research team. The role emphasizes translating computational predictions into actionable design parameters and collaborating with experimental colleagues in a growing program

Qualifications

• Ph.D. in Computational Chemistry, Biophysics, or Protein Engineering (MS with 5+ years experience may be considered).
• Experience with regression, optimization, protein language or transformer models to analyze large datasets.
• Experience using generative and physics-based models for de-novo protein design and in-silico screening.
• Strong understanding of protein structure–function relationships.
• Programming in Python and/or C++/Rust for pipeline development and custom script generation.
• Experience automating computational workflows on HPC to reduce design turnaround time.
• U.S. Citizenship required due to government facility access.

Responsibilities

• Machine Learning for Data Analysis: Analyze large protein function datasets and generate sequences with predicted improvements in performance.
• Computational Design & Generative AI: Deploy design suites (RFDiffusion, Rosetta, LigandMPNN) to create novel binding pockets for polyvalent metals.
• Structural Bioinformatics: Develop high-throughput in-silico workflows for evaluating protein scaffold quality.
• Interdisciplinary Interface: Translate predictions into design parameters and assess experimental data within design-test-learn workflows.

Skills

Regression models

Optimization

Protein language models

Transformer models

Generative models

Python

C++/Rust

High-performance computing

Education

PhD in Computational Chemistry

PhD in Biophysics

MS with 5+ years experience accepted

Tools

RFDiffusion

Rosetta

LigandMPNN

Job description

Position Overview

The Biological Materials and Processing Research Team is seeking a Computational Protein Engineer to lead the design and optimization of proteins for use in novel metal separation technologies that address the nation’s growing need for critical materials. This role will focus on de novo protein design and optimizing protein performance and will involve using generative protein design software, machine learning methodologies for analysis of large experimental datasets, and other computational workflows. The successful candidate will play a foundational role in a growing research program and will have the opportunity for significant project ownership. They will join a group of collaborative scientists with diverse skill sets and should have strong communication skills, a collaborative mindset, and an enthusiasm for innovative research.

Key Responsibilities

• Machine Learning for Data Analysis: Implement and fine-tune machine learning algorithms to analyze large protein function datasets and generate sequences with predicted improvements in performance.
• Computational Design & Generative AI: Deploy advanced protein design suites (e.g., RFDiffusion, Rosetta, LigandMPNN) to architect novel binding pockets for polyvalent metals.
• Structural Bioinformatics: Develop and implement high-throughput workflows for in-silico assessment of the quality of engineered protein scaffolds.
• Interdisciplinary Interface: Translate computational predictions into actionable design parameters and assess resulting experimental data in collaboration with experimental team members as a part of design-test-learn workflows.

Required Qualifications

• Education: Ph.D. in Computational Chemistry, Biophysics, Protein Engineering, or a related field. (Candidates with an M.S. and 5+ years of specialized experience will be considered).
• Technical Expertise: Extensive experience with the use of regression, optimization, protein language, or transformer models to analyze large datasets.
• Experience using generative and physics-based models for de-novo protein design and in-silico screening.
• Strong understanding of protein structure-function relationships.
• Programming: Fluency in Python and/or C++/Rust for pipeline development and custom script generation.
• Experience automating computational workflows and implementing them on high-performance computers to reduce design turnaround time.
• Citizenship: U.S. Citizenship is required due to government facility access requirements.

Preferred Skills

• Technical Project Coordination: Experience coordinating work done by third parties (e.g. CROs, academic collaborators, and other external partners).
• Metalloproteins: Familiarity with the structure and function of metalloproteins.
• QM Modeling: Experience with quantum mechanical modeling of protein-metal interactions.
• Laboratory Familiarity: Experience with (or willingness to learn) theory behind experimental techniques for characterizing protein function.
• ITAR Requirement: This position requires access to information that is subject to compliance with the International Traffic Arms Regulations (“ITAR”) and/or the Export Administration Regulations (“EAR”). In order to comply with the requirements of the ITAR and/or the EAR, applicants will be asked to provide specific documentation to verify U.S. person status under the ITAR and the EAR. A “U.S. person” according to their definition is a U.S. citizen, U.S. lawful permanent resident (green card holder), or protected individual such as a refugee, or asylee. See 22 CFR § 120.15. Some positions will require current U.S. Citizenship due to contract requirements.

Benefits

• AV offers an excellent benefits package including medical, dental vision, 401K with company matching, a 9/80 work schedule and a paid holiday shutdown.

For more information about our company benefit offerings please visit: http://www.avinc.com/myavbenefits.

We also encourage you to review our company website at http://www.avinc.com to learn more about us.

Who We Are

Based in California, AeroVironment (AVAV) is a global leader in unmanned aircraft systems (UAS) and tactical missile systems. Founded in 1971 by celebrated physicist and engineer, Dr. Paul MacCready, we’ve been at the leading edge of technical innovation for more than 45 years. Be a part of the team that developed the world’s most widely used military drones and created the first submarine-launched reconnaissance drone, and has seven innovative vehicles that are part of the Smithsonian Institution’s permanent collection in Washington, DC. Join us today in developing the next generation of small UAS and tactical missile systems that will deliver more actionable intelligence to our customers so they can proceed with certainty – and succeed.

What We Do

Building on a history of technological innovation, AeroVironment designs, develops, produces, and supports an advanced portfolio of unmanned aircraft systems (UAS) and tactical missile systems. Agencies of the U.S. Department of Defense and allied military services use the company’s hand-launched UAS to provide situational awareness to tactical operating units through real-time, airborne reconnaissance, surveillance, and target acquisition.

We are proud to be an EEO/AA Equal Opportunity Employer, including disability/veterans. AeroVironment, Inc. is an Equal Employment Opportunity (EEO) employer and welcomes all qualified applicants. Qualified applicants will receive fair and impartial consideration without regard to race, sex, color, religion, national origin, age, disability, protected veteran status, genetic data, sexual orientation, gender identity or other legally protected status.

ITAR About AV

AV isn’t for everyone. We hire the curious, the relentless, the mission-obsessed. The best of the best. We don’t just build defense technology—we redefine what’s possible. As the premier autonomous systems company in the U.S., AV delivers breakthrough capabilities across air, land, sea, space, and cyber. From AI-powered drones and loitering munitions to integrated autonomy and space resilience, our technologies shape the future of warfare and protect those who serve. Founded by legendary innovator Dr. Paul MacCready, AV has spent over 50 years pushing the boundaries of what unmanned systems can do. Our heritage includes seven platforms in the Smithsonian—but we’re not building history, we’re building what’s next. If you're ready to build technology that matters—with speed, scale, and purpose—there’s no better place to do it than AV.

Careers at AeroVironment