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We are seeking a highly motivated and experienced Senior Scientist with expertise in computational biology, protein structural modeling and engineering, and machine learning to join the Data Science & Algorithms Team. This role focuses on designing and optimizing protein binders with high affinity for N-terminal amino acid targets, a critical component of our Next-Generation Protein Sequencing kit.

You will work at the intersection of protein engineering, machine learning, and structural biology, leveraging state-of-the-art algorithms experimental feedback to develop novel protein scaffolds with tailored binding characteristics.

The ideal candidate will have a deep background in Computational Biology, Bioengineering, Structural Biology, or a related field with 5+ years of relevant academic or industry experience. The candidate also must have a strong knowledge of programming languages (e.g. Python, Bash) and protein modeling software (e.g. AlphaFold, ProteinMPNN). Knowledge of fine-tuning or generating new machine-learning models is a plus.

As part of our team, your core responsibilities will be: 

+ Design, model, and computationally screen protein binders for selective binding to N-terminal amino acid motifs.

+ Develop and optimize binder scaffolds using a combination of **structure-based design, ML-driven design** , and **generative protein modeling tools** .

+ Collaborate with wet-lab teams to iteratively test, validate, and refine designs using experimental feedback.

+ Innovate new computational pipelines for high-throughput protein binder discovery.

+ Evaluate binding energetics, specificity, and structural feasibility using in silico approaches.

Qualifications

+ PhD. in Computational Biology, Bioengineering, Structural Biology, or a related computational/scientific field

+ Proven expertise in protein structure prediction and design using cutting-edge modeling software (AlphaFold, ProteinMPNN, RFDiffusion, ESM, Rosetta, etc.)

+ Strong understanding of protein-protein and protein-peptide interactions, as well as hands-on experience conducting in silico analyses to evaluate these interactions

+ Experience developing **custom computational methods** or ML approaches to guide design toward desired structural/functional properties

+ Proficient in programming with **Python** (preferred) and/or other scripting languages such as **Bash** ; familiarity with **JupyterLab** , **Jupyter Notebooks** , or similar virtual notebook environments for data analysis, interactive modeling, and prototyping.

+ Strong analytical thinking and practical problem-solving skills, including the ability to break problems into logical subproblems and devise efficient and flexible solutions

+ Excellent scientific communication and documentation skills, including data summarization and visualization using Python

Ideally, you also have these skills/experiences/attributes (but it’s ok if you don’t!):

+ Publications showcasing the use of advanced protein design tools (e.g., AlphaFold, RFDiffusion, ProteinMPNN) to develop proteins with targeted functions or novel structural features

+ Experience **designing binders** against **unstructured peptide regions** , including terminal epitopes or motifs

+ Experience with **ML model development or fine-tuning** , particularly for structure-function prediction or generative protein design.

+ Experience integrating **experimental feedback loops** into computational pipelines to improve design success.

+ Familiarity with **GPU-accelerated computing** and scaling workflows using **HPC or cloud resources** .

+ Experience with Git

The estimated base salary range for this role based in the United States of America is: $130,000 - $155,000. Compensation decisions are dependent on several factors including, but not limited to, level of the position, an individual’s skills, knowledge and abilities, location where the role is to be performed, internal equity, and alignment with market data. Additionally, all full-time employees are eligible for our discretionary bonus program and equity as part of the compensation package.

Quantum-Si does not accept agency resumes.

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability or Veteran status. All your information will be kept confidential according to EEO guidelines.