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Silico Protein Design information

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$42K

$114.5K

$201.5K

How much do silico protein design jobs pay per year?

As of Jun 15, 2026, the average yearly pay for silico protein design in the United States is $114,491.00, according to ZipRecruiter salary data. Most workers in this role earn between $83,500.00 and $144,000.00 per year, depending on experience, location, and employer.

What are some common challenges faced by professionals in Silico Protein Design and how can they be addressed?

Professionals in Silico Protein Design often encounter challenges such as handling the complexity of protein structures, ensuring computational predictions translate effectively to laboratory results, and keeping up with the rapid evolution of bioinformatics tools. To address these, it's important to work closely with experimental teams, stay updated on the latest software and databases, and continuously refine computational models based on feedback from experimental validation. Collaboration and ongoing learning are key to overcoming these hurdles and advancing in this innovative field.

What is silico protein design?

Silico protein design refers to the use of computer algorithms and software to model, predict, and create new protein structures with desired functions. This process allows scientists to simulate how amino acid sequences will fold and behave, enabling the design of proteins for specific applications such as therapeutics, enzymes, or materials. By leveraging computational tools, researchers can save time and resources compared to traditional experimental methods, making the protein engineering process more efficient and innovative.

What is the difference between Silico Protein Design vs Protein Biochemist?

AspectSilico Protein DesignProtein Biochemist
Required CredentialsDegree in Bioinformatics, Computational Biology, or related fieldDegree in Biochemistry, Molecular Biology, or related field
Work EnvironmentPrimarily computational, using software and modeling toolsLaboratory-based, involving wet lab experiments
Industry UsageResearch and development in biotech, pharmaceuticals, academiaResearch, diagnostics, and product development in biotech and pharma

Silico Protein Design focuses on using computational methods to predict and engineer protein structures, while Protein Biochemists perform laboratory experiments to study protein functions. Both roles are essential in biotech and pharma industries but differ mainly in their approach—digital modeling versus wet lab work.

What are the key skills and qualifications needed to thrive as an In Silico Protein Designer, and why are they important?

To thrive as an In Silico Protein Designer, you need a solid background in molecular biology, computational modeling, and protein biochemistry, typically supported by a relevant advanced degree. Familiarity with bioinformatics tools, molecular modeling software (like Rosetta or PyMOL), and programming languages such as Python is crucial. Strong analytical thinking, attention to detail, and effective collaboration skills help you interpret complex data and work within multidisciplinary teams. These competencies enable the accurate design and optimization of proteins for research and therapeutic applications, ensuring innovation and scientific rigor.
Infographic showing various Silico Protein Design job openings in the United States as of June 2026, with employment types broken down into 100% Full Time. Highlights an 86% Physical, 4% Hybrid, and 10% Remote job distribution, with an average salary of $114,491 per year, or $55 per hour.

Senior Scientist, Computational Protein Design

Abiologics

Boston, MA

$99K - $135K/yr

Other

Medical, Retirement

Posted 18 days ago

Job description

About Abiologics 

Abiologics is a Flagship Pioneering company developing Synteins - a transformative class of fully synthetic proteins composed entirely of artificial building blocks such as D-amino acids and non-canonical residues. SynteinsTM are designed to transcend the limitations of traditional biologics, with improved oral stability, immune evasion, and metabolic durability - all while being fully programmable by design. 

Powered by a proprietary AI-enabled discovery platform, Abiologics integrates generative design, automated synthesis, and rapid experimental screening to enable iterative optimization at scale. 

Position Summary 

We are seeking a Protein Design Scientist to join the Computational Protein Design team and help drive structure-based design and optimization of synthetic proteins. This is a highly interdisciplinary role at the interface of computational design, structural biology, and protein engineering. 

Ideal candidates have deep experience in de novo protein design, miniproteins, and binders engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment. 

Key Responsibilities 

  • Design and execute SynteinsTM engineering campaigns to generate drug candidates. 
  • Create computational design strategies to deliver drug candidates drawing from array of ML tools and Rosetta scripts. 
  • Collaborate with computation, chemistry, and experimental biology teams to optimize designs for function, solubility, and stability. 
  • Integrate structural and biophysical data (e.g., binding, CD, HDX-MS, CryoEM) into iterative optimization cycles 

Qualifications 

Required 

  • PhD in structural biology, biophysics, protein design, or related field 
  • 2+ years of hands-on experience in structure-guided protein design 
  • Demonstrated proficiency with modern structure prediction and design tools such as RFdiffusion, proteinMPNN, AF2, Boltz2, BoltzGen, Rosetta or equivalent SOTA tools for in-silico protein engineering. 
  • Strong understanding of the biophysics of protein folding and interface energetics 
  • Demonstrated ability to progress designs from concept to experimental testing 
  • Excellent communication skills  

Preferred 

  • Experience designing minibinders or proteins <100 AAs 
  • Familiarity with non-canonical amino acid design 
  • Familiarity with molecular dynamics tools. 
  • Exposure to high-throughput or automated protein engineering environments 
  • Prior work on platform-based or early-stage biotech teams 

Why Join Abiologics 

  • Help invent a new class of programmable synthetic proteins 
  • Be part of a high-velocity discovery platform with real-time synthesis and screening 
  • Collaborate with a deeply interdisciplinary, mission-driven team 
  • Redefine the limits of what proteins can do 

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity's most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE's "Change the World" list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company's annual list of the World's Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, "FSP") do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

 #LI-MB1

The salary range for this role is $146,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Abiologics, Inc currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc's good faith estimate as of the date of publication and may be modified in the future.

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