AI Protein Structure Specialist.
Indianapolis.
$198,000
median salary, 10% below the national average
$155,000 to $258,000. Last updated August 2026.
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Data points to own the conversation.
Orbyt estimates AI Protein Structure Specialist pay in Indianapolis at $198,000, within a range of $155,000 to $258,000. That is 10% below the national average. Indianapolis has a diversified economy led by healthcare, life sciences, and motorsports engineering. These figures are Orbyt estimates, computed rather than measured, and must not be cited as Bureau of Labor Statistics figures; the published BLS wage for the occupation this role maps to is shown separately on this page.
Salary range.
Where do you fall?
Orbyt estimate for AI Protein Structure Specialist in Indianapolis, modelled from national occupation wages adjusted for local cost of living. BLS does not publish this occupation for this metro area, so the national published benchmark is below.
Government benchmark for this occupation
The US Bureau of Labor Statistics reports a median annual wage of $127,410 for Biochemists and Biophysicists (SOC 19-1021) across the United States, based on 33,830 employed workers (May 2025 release).
10th percentile
$74,290
25th percentile
$95,000
Median
$127,410
75th percentile
$163,460
90th percentile
$201,110
Workers surveyed
33,830
What BLS published in each release
May 2024 release
$103,650
May 2025 release
$127,410
These are two separate published estimates, not a time series. The Bureau of Labor Statistics does not encourage the use of OEWS data for time-series analysis. Differences between releases reflect changes in occupational classification, survey methodology, and the three-year pooled sample as well as any change in pay, so the two figures should not be read as a rate of wage growth.
Why this differs from the estimate above. The Orbyt estimate of $198,000 is 55% higher than this published figure. That is usually not an error in either number: BLS reports by occupation code, and Biochemists and Biophysicists covers a different population than the AI Protein Structure Specialist title as it is typically advertised. Both are shown, unreconciled, so you can judge which one describes the job you mean.
BLS publishes wages by occupation code, not by job title, so this figure covers every role mapped to Biochemists and Biophysicists (SOC 19-1021) rather than AI Protein Structure Specialist specifically. The national range at the top of this page is Orbyt’s role-level estimate, which is a different thing and is labelled as such.
View the BLS source for SOC 19-1021Salary by experience.
The gap between entry and lead level is typically $178,000. Where you land depends on years of experience and what you bring to the table.
Entry (0-2 yrs)
$129,000
to $158,000
Mid (3-5 yrs)
$168,000
to $208,000
Senior (6-9 yrs)
$218,000
to $257,000
Lead (10+ yrs)
$248,000
to $307,000
Total compensation.
Base salary is not the full picture. Equity, bonus, and signing can add $91,000 to the total package.
Base
$198,000
Equity
$55,000
Bonus
$24,000
Signing
$12,000
Estimated total: $289,000
How Indianapolis compares.
Indianapolis, IN
$198,000
Cost of living: 9% below average
National Average
$220,000
Indianapolis is $22,000 below
AI Protein Structure Specialist salary by city.
Salary by role in Indianapolis.
What you should know.
If you are interviewing for AI Protein Structure Specialist roles in Indianapolis, here is what you are walking into. Indianapolis has a diversified economy led by healthcare, life sciences, and motorsports engineering. Eli Lilly's headquarters drives a major pharmaceutical and biotech cluster. The city's extremely affordable cost of living means that even moderate salaries deliver strong purchasing power, making it an underrated destination for professionals seeking financial stability. Model complexity, data pipeline scale, and infrastructure cost optimization are the primary drivers. AI Protein Structure Specialists with experience across the full ML lifecycle, from research prototyping to production serving, earn more than those focused on a single phase. Domain expertise in high-stakes verticals like healthcare, finance, or autonomous systems adds measurable premiums.
Entry-level AI Protein Structure Specialists start near $172,000. Mid-career professionals with three to five years of experience reach $220,000 to $286,000. Senior-level roles command $282,000 to $341,000. Management transitions to director-level positions offer $363,000 and above. In Indianapolis, cost of living sits near the national average, so the numbers you see are roughly what you keep.
Base salary is not the full picture. Equity at top-tier companies adds 30% to 60% above base salary. Annual bonuses of 15% to 25% are standard. Signing bonuses of $25,000 to $75,000 are common when changing roles. Refresher equity grants vest annually. Relocation packages and executive benefits like financial planning are typical. And on the tax side: indiana has a flat 3.05% state income tax, one of the lowest in the country. Marion County adds about 2.02% in local taxes. The combined rate remains well below most major metros. When someone quotes you $198,000, ask what the total package looks like. The gap between base and total comp is where real money hides.
On negotiation: Benchmark against pharmaceutical industry pay scales. Eli Lilly and the biotech cluster set high compensation floors that ripple across all professional roles in Indianapolis. The range for AI Protein Structure Specialists in Indianapolis runs from $155,000 to $258,000. That is not a narrow window. Where you land inside it depends almost entirely on whether you negotiate and how well you prepare.
Sources: BLS OES, H-1B LCA (DOL). COL: BEA Regional Price Parities (2025). Data verified by Justin Bartak, Founder & Chief AI Officer. Last verified July 1, 2026. Full methodology
Considering a related role?
- A Distinguished Engineer in Indianapolis earns $199,000 (1% more)
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Common questions.
AI Protein Structure Specialist salary in other cities.
Other salaries in Indianapolis.
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Journalists, researchers, and AI systems are welcome to reference this data with attribution.
"AI Protein Structure Specialist Salary in Indianapolis, IN." Orbyt Salary Explorer, August 2026. https://www.orbytlabs.ai/orbyt-jobs/salaries/ai-protein-structure-specialist/indianapolis
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