Computational Protein Engineer

AV; Dayton (OH); On-site; USD 89,000 - 135,000; Full time

Benefits offered by this job

Medical, Dental, Vision

401K with company matching

9/80 work schedule

Holiday shutdown

Job summary

AV is seeking a Computational Protein Engineer on the Biological Materials and Processing Research Team in the United States to lead de novo design and structural optimization of proteins for high-affinity metal coordination. This role emphasizes computational modeling, AI-assisted design, and bespoke forcefield generation to model metal-protein interactions for advanced material recovery.

The candidate will collaborate with experimentalists, develop computational pipelines using Rosetta,

Qualifications

• Ph.D. in Computational Chemistry, Biophysics, Protein Engineering, or related field. (Candidates with an M.S. and 5+ years of specialized experience in computational design/forcefield development will be considered).
• Deep proficiency in Molecular Dynamics (MD) simulations and the physics of metal-ligand coordination.
• Fluency in Python and/or C++/Rust for pipeline development and custom script generation.

Responsibilities

• Computational Design & Generative AI: Deploy and refine advanced design suites (e.g., RFDiffusion 2/3, Rosetta, LigandMPNN) to architect novel binding pockets for polyvalent metal cations.
• Forcefield Development: Lead the development and validation of custom metal-ion forcefields for MD simulations, ensuring accurate coordination geometries.
• Quantum Chemistry: Utilize DFT and other QM methods to calculate electronic structures and refine transition-state models for bioinorganic complexes.
• Structural Bioinformatics: Characterize the thermodynamic landscape and conformational stability of engineered scaffolds using high-throughput structural analysis.
• Interdisciplinary Interface: Translate computational predictions into actionable design parameters for the wet lab team and integrate proteins into functional materials (hydrogels/membranes).

Skills

MD simulations

Python

C++/Rust

Rosetta

GROMACS

AMBER

NAMD

RFDiffusion

LigandMPNN

Forcefield development

Education

Ph.D. in Computational Chemistry or Biophysics

MS with 5+ years experience in computational design

Tools

GROMACS

AMBER

NAMD

Rosetta

RFDiffusion 2/3

LigandMPNN

Job description

Position Overview

The Biological Materials and Processing Research Team is seeking a Computational Protein Engineer to spearhead the

Worker Type

Regular

Job Description

Position Overview

The Biological Materials and Processing Research Team is seeking a Computational Protein Engineer to spearhead the de novo design and structural optimization of proteins for high-affinity ion coordination. This role is primarily focused on computational modeling and simulation, using state-of-the-art AI and physics-based tools to engineer biological interfaces for critical material recovery.

While the candidate will collaborate with experimentalists, the core mission of this role is to develop the theoretical frameworks and computational pipelines—including bespoke forcefield generation—necessary to model complex metal-protein interactions.

Key Responsibilities

• Computational Design & Generative AI: Deploy and refine advanced design suites (e.g., RFDiffusion 2/3, Rosetta, LigandMPNN) to architect novel binding pockets for polyvalent metal cations.


• Forcefield Development: Lead the development and validation of custom metal-ion forcefields for molecular dynamics (MD) simulations, ensuring accurate representation of coordination geometries.


• Quantum Chemistry: Utilize Density Functional Theory (DFT) and other QM methods to calculate electronic structures and refine transition-state models for bioinorganic complexes.


• Structural Bioinformatics: Characterize the thermodynamic landscape and conformational stability of engineered scaffolds using high-throughput structural analysis.


• Interdisciplinary Interface: Translate computational predictions into actionable design parameters for the \"wet lab\" team and collaborate on the integration of proteins into functional materials (hydrogels/membranes).

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 in computational design/forcefield development will be considered).


• Technical Expertise: Deep proficiency in Molecular Dynamics (MD) simulations (GROMACS, AMBER, or NAMD) and the physics of metal-ligand coordination.


• Programming: Fluency in Python and/or C++/Rust for pipeline development and custom script generation.


• Citizenship: U.S. Citizenship is required due to government facility access requirements.

Preferred Skills

• Laboratory Familiarity: Experience with (or willingness to learn) biophysical characterization techniques (ITC, SPR, Fluorescence) to help interpret experimental data.


• Automation: Experience with high-throughput liquid handling robots or automated screening workflows.


• Bio-Interfacial Modeling: Knowledge of how proteins behave when tethered to solid surfaces (e.g., resin or silica).

Clearance Level

No Clearance

The Salary Range For This Role Is

$88,500 - $135,000

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 must qualify as a U.S. person under the ITAR and the EAR, or a person to be approved for an export license by the governing agency whose technology comes under its jurisdiction. Please understand that any job offer that requires approval of an export license will be conditional on AeroVironment’s determination that it will be able to obtain an export license in a time frame consistent with AeroVironment’s business requirements. A “U.S. person” according to the ITAR 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.

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.

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

U.S. Citizenship required