Computational Protein Engineer

InvestedintheMission; Bath Township (OH); On-site; USD 150,000 - 190,000; Full time

Benefits offered by this job

Medical benefits

Dental benefits

Vision benefits

401K with company match

9/80 work schedule

Paid holiday shutdown

Job summary

AeroVironment seeks a Computational Protein Engineer to lead de novo protein design and optimization for metal separation technologies. You will work with machine learning, generative design tools, and large experimental datasets to drive protein performance improvements.

Join a collaborative team of scientists in a government-facing facility, with opportunities for project ownership and cross-disciplinary collaboration across computational and experimental teams.

Qualifications

• PhD in computational fields or related with strong protein design background.
• Experience with regression/optimization for large datasets and protein structure–function knowledge.
• Fluency in Python; C++/Rust for pipelines; HPC workflow automation.

Responsibilities

• Machine Learning for data analysis to generate sequences with improvements.
• Computational design using RFDiffusion, Rosetta, LigandMPNN to create novel binding pockets.
• High-throughput in-silico workflows to assess engineered protein scaffolds.
• Translate computational predictions into design parameters and collaborate with experimental team.

Skills

Regression & optimization

Protein language models

Transformer models

Python/C++/Rust

Education

PhD in Computational Chemistry/Biophysics/Protein Engineering

MS with 5+ years experience

Tools

RFDiffusion

Rosetta

LigandMPNN

Job description

Worker Type

Regular

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.

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.