Computational Enzyme Engineer

We have an opening for a Computational Enzyme Engineer to join ongoing projects developing innovative biologics therapeutics and vaccines against infectious diseases as part of the Center for Predictive Bioresilience (CPB). CPB is an exciting and fast-paced engineering center combining predictive computational modeling machine learning and experimental biology to develop medical countermeasures. 

You will be responsible for leveraging cutting-edge computational tools and algorithms like RFDiffusion RosettaFold ProteinMPNN and AlphaFold to design and engineer proteins and enzymes with enhanced activity specificity and stability. This role involves building and training predictive models for enzyme engineering using machine learning and deep learning tools as well as performing extensive data analysis on experimental protein engineering datasets (including activity and sequence/structure information) to continuously refine and improve these models. You will also develop and implement computational methods utilizing 3D structures and/or sequences to optimize enzyme characteristics and will design protein libraries and datasets for high-throughput screening. Collaboration with interdisciplinary teams of biologists chemists and other engineers is crucial to integrate computational insights seamlessly with experimental design and execution. This position will be in the Computational Engineering Division (CED) within the Engineering Directorate matrixed to the CPB.

In this role you will

• Utilize advanced computational tools and algorithms (such as RFDiffusion RosettaFold ProteinMPNN and AlphaFold) to contribute to and actively participate in the design and engineering of novel proteins and enzymes with desired properties (e.g. enhanced activity specificity or stability).
• Collaborate with team members and participate in building and training predictive models for enzyme engineering using techniques like machine learning and deep learning including providing input recommending enhancements and solving problems of moderate complexity.
• Analyze large datasets from experimental protein engineering efforts (including enzyme activity data and sequence/structure information) to refine and improve computational models.
• Develop and implement moderately complex computational methods potentially utilizing 3D structures and/or sequences as input to enhance enzyme stability solubility and activity.
• Document methods and implementation methodologies activities sequences and requirements in both informal and formal reports and presentations.
• Design protein libraries and datasets for high-throughput screening and hit identification.
• Analyze data deliver results engage with and participate in a talented team to identify create implement benchmark and scale cutting-edge techniques that integrate biophysics and AI for computational protein design with a focus on therapeutic modalities including antibodies.
• Design test deploy and maintain high-quality pipelines on HPC and cloud infrastructures ensuring scalable and robust solutions.
• Balance multiple projects/tasks and priorities of customers and partners to ensure deadlines are met while working independently with limited direction within the scope of the assignment.n.
• Perform other duties as assigned.

Additional job responsibilities at the SES.3 level

• Lead projects that develop advanced computational protein design strategies to meet diverse scientific and technical challenges.
• Independently determine the appropriate technical objectives criteria and approaches to satisfy and execute project deliverables.
• Provide solutions to abstract and complex problems using in-depth analysis drawing from advanced level technical knowledge and best practices and collaborate in the development of innovative methods/technology to guide and ensure successful completion of project and organizational goals.
• Represent the organization as the primary technical contact by sharing relevant knowledge providing opinions and recommendations and exerting influence to fulfill deliverables as a team.
• Lead and mentor junior staff and students.

Qualifications :

• Masters degree in biochemistry biophysics bioinformatics computational chemistry computer science AI/ML or a related technical discipline focused on solving biological problems using computational approaches or the equivalent combination of education and related experience.
• Comprehensive knowledge of or experience in developing and implementing novel methods and algorithms for computational protein design.
• Proficiency in programming with languages such as Python C/C or Java.
• Proficient written and verbal communication skills necessary to work and collaborate effectively in a multi-disciplinary environment and to present and explain technical information.
• Demonstrated strong record of documentation of executed work.
• Ability to prioritize balance and keep several parallel threads of work in simultaneous smooth motion.

Additional qualifications at the SES.3 level

• Advanced level knowledge and significant experience in computational protein design or a related technical field.
• Ability to independently develop and execute complex analyses and to prepare and finalize tailored reports.
• Significant experience leading interdisciplinary teams including setting clear expectations delegating to subordinates and peers and ensuring successful timely completion of objectives.
• Advanced verbal and written communication facilitation and interpersonal skills necessary to effectively collaborate and lead in a team environment and to present and explain technical information influence and guide team members and provide advice to management.

Qualifications We Desire

• PhD in biochemistry biophysics bioinformatics computational chemistry computer science AI/ML or a related technical discipline focused on solving biological problems using computational approaches.
• Demonstrated understanding of fundamental biochemistry and enzyme engineering concepts including kinetics reaction mechanisms transition states and rational design.
• Experience with classic computational approaches to estimating enzymatic properties such as thermodynamic stability and net charge and mathematical modeling of enzyme reaction dynamics.
• Familiarity with non-canonical amino acids and their use in protein design.
• Experience with design and modeling tools such as Rosetta RFDiffusion ProteinMPNN AlphaFold etc.
• Background in developing generative AI structure- or sequence-based methods for therapeutic protein design.
• Familiarity with training generative AI models applying bioinformatics approaches to sequence analysis and managing large databases of protein structures and sequences.
• Experience with modern deep learning frameworks (e.g. PyTorch JAX SageMaker) and cloud services (e.g. Git Docker AWS Batch Step Functions EKS).

Additional Information :

#LI-Hybrid

Position Information

This is a Flexible Term appointment which is for a definite period not to exceed six years.  If final candidate is a Career Indefinite employee Career Indefinite status may be maintained (should funding allow).

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  Remote Work :

  No

  
  

  Employment Type :

  Full-time