Senior Scientist, Computational Biology

Lensa; San Diego (CA); On-site; USD 130,000 - 155,000; Full time

Job summary

Lensa is seeking a Senior Scientist with a strong background in computational biology to join their Data Science team in San Diego. The role involves designing and optimizing protein binders for cutting-edge protein sequencing technology. Candidates should possess a deep understanding of structural biology, machine learning, and computational methods, with at least 5 years of experience in relevant fields.

Benefits

Discretionary bonus program

Equity options

Qualifications

• 5+ years of relevant academic or industry experience.
• Proficient in programming with Python and scripting languages.
• Experience with protein modeling software is essential.

Responsibilities

• Design and computationally screen protein binders for selective binding.
• Collaborate with wet-lab teams for validation and refinement.
• Innovate computational pipelines for protein binder discovery.

Skills

Protein structure prediction

Computational methods

Machine learning

Analytical thinking

Problem-solving

Education

PhD in Computational Biology

Bioengineering

Structural Biology

Tools

AlphaFold

ProteinMPNN

Python

Bash

JupyterLab

Job description

1 day ago Be among the first 25 applicants

Get AI-powered advice on this job and more exclusive features.

Lensa partners with DirectEmployers to promote this job for Quantum-Si.

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.

If you have questions about this posting, please contact [e-mail]

Seniority level

• Seniority level

  Mid-Senior level

Employment type

• Employment type

  Full-time

Job function

• Job function

  Research, Analyst, and Information Technology

• Industries

  IT Services and IT Consulting

Referrals increase your chances of interviewing at Lensa by 2x

Get notified about new Senior Scientist jobs in San Diego, CA.

Director/Senior Director, Clinical Scientist

Project to Senior Level Engineer/Geologist/Environmental Scientist

Scientist, Analytical Chemistry Research

San Diego, CA $88,000.00-$127,550.00 12 hours ago

Clinical Scientist/Senior Clinical Scientist

San Diego County, CA $146,700.00-$175,000.00 1 month ago

Senior Scientist, Analytical Development

Principal Research Scientist, Formulations

Senior Scientist, Computational Chemistry

San Diego Metropolitan Area $155,000.00-$184,000.00 6 days ago

Principal Scientist, Analytical Development

Analytical Development Research Scientist

TEMP - Scientist / Sr. Scientist, Bioanalytical Chemist

Analytical Development Principal Research Scientist

Principal Scientist, Medicinal Chemistry

San Diego, CA $105,890.00-$189,545.00 17 hours ago

TEMP - Scientist, Analytical Chemistry, Research

Associate Principal Scientist, Computational Chemistry

San Diego Metropolitan Area $176,000.00-$198,000.00 5 days ago

Principal Scientist Early Discovery, Non Clinical Safety Lead

Principal Scientist Medicinal Chemistry - San Diego, CA

Scientist/Senior Scientist, Computational Drug Design

Principal Scientist, Discovery Biologics

We’re unlocking community knowledge in a new way. Experts add insights directly into each article, started with the help of AI.