Computational Protein Engineer

AeroVironment, Inc.; Bath Township (OH); On-site; USD 150,000 - 180,000; Full time

Benefits offered by this job

Medical, dental, vision

401K with company matching

9/80 work schedule

Paid holiday shutdown

Job summary

AeroVironment, Inc. seeks a Computational Protein Engineer to lead de novo protein design and optimization for metal separation technologies. The role focuses on machine learning, generative design, and high-throughput in-silico workflows, with collaboration across experimental and computational teams.

You will implement design pipelines on high-performance computers, using Rosetta, RFDiffusion, and LigandMPNN to engineer protein scaffolds and binding pockets for polyvalent metals. U.S.

Qualifications

• PhD in Computational Chemistry, Biophysics, Protein Engineering or related field.
• Strong experience with regression/optimization or transformer models for large datasets.
• Proficiency in Python and/or C++/Rust for pipelines and automation.

Responsibilities

• Lead design and optimization of proteins for metal separation technologies.
• Apply generative AI and machine learning to design novel binding pockets.
• Develop high-throughput in-silico workflows for protein evaluation.
• Collaborate with experimental team to translate predictions into designs.

Skills

Machine learning

Protein design

Python

High performance computing

Data analysis

Education

PhD in Computational Chemistry/Biophysics/Protein Engineering

MS with 5+ years specialized experience

Tools

Rosetta

RFDiffusion

LigandMPNN

Job description

Worker TypeRegularJob DescriptionPosition OverviewThe 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 ResponsibilitiesMachine 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 QualificationsEducation: 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 SkillsTechnical 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 interactionsLaboratory 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.Principals only need apply. NO agencies please.Who We AreBased 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 DoBuilding 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