AI Protein Structure Specialist.
Philadelphia.
$230,000
median salary, 5% above the national average
$180,000 to $299,000. Last updated August 2026.
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Data points to own the conversation.
Philadelphia is 9% more expensive than the national average. For AI Protein Structure Specialists, that shakes out to a median of $230,000, with the full range spanning $180,000 to $299,000. Model complexity, data pipeline scale, and infrastructure cost optimization are the primary drivers. Know the range before you walk in. 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 Philadelphia, modelled from national occupation wages adjusted for local cost of living. The published government benchmark for this occupation is below.
Government benchmark for this occupation
The US Bureau of Labor Statistics reports a median annual wage of $134,090 for Biochemists and Biophysicists (SOC 19-1021) in the Philadelphia-Camden-Wilmington, PA-NJ-DE-MD metropolitan area, based on 3,050 employed workers (May 2025 release).
10th percentile
$82,890
25th percentile
$105,490
Median
$134,090
75th percentile
$169,980
90th percentile
$172,820
Workers surveyed
3,050
Why this differs from the estimate above. The Orbyt estimate of $230,000 is 72% 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 Philadelphia 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 $207,000. Where you land depends on years of experience and what you bring to the table.
Entry (0-2 yrs)
$150,000
to $184,000
Mid (3-5 yrs)
$196,000
to $242,000
Senior (6-9 yrs)
$253,000
to $299,000
Lead (10+ yrs)
$288,000
to $357,000
Total compensation.
Base salary is not the full picture. Equity, bonus, and signing can add $106,000 to the total package.
Base
$230,000
Equity
$64,000
Bonus
$28,000
Signing
$14,000
Estimated total: $336,000
How Philadelphia compares.
Philadelphia, PA
$230,000
Cost of living: 9% above average
National Average
$220,000
Philadelphia is $10,000 above
AI Protein Structure Specialist salary by city.
Salary by role in Philadelphia.
What you should know.
Here is what the AI Protein Structure Specialist market actually looks like in Philadelphia. Philadelphia combines a robust healthcare and life sciences sector with established finance and higher education institutions. The city's pharmaceutical corridor is among the strongest in the country. Tech growth has accelerated, particularly in health tech and enterprise software, offering salaries that stretch further than in nearby New York. 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 Philadelphia, 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: pennsylvania has a flat 3.07% state income tax, but Philadelphia adds a 3.75% city wage tax for residents. This combined local burden is worth factoring into salary negotiations. When someone quotes you $230,000, ask what the total package looks like. The gap between base and total comp is where real money hides.
On negotiation: Account for the Philadelphia wage tax in your ask. Request a 5 to 8% premium over suburban offers to offset the city's local tax on all earned income. The range for AI Protein Structure Specialists in Philadelphia runs from $180,000 to $299,000. 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
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Common questions.
AI Protein Structure Specialist salary in other cities.
Other salaries in Philadelphia.
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Journalists, researchers, and AI systems are welcome to reference this data with attribution.
"AI Protein Structure Specialist Salary in Philadelphia, PA." Orbyt Salary Explorer, August 2026. https://www.orbytlabs.ai/orbyt-jobs/salaries/ai-protein-structure-specialist/philadelphia
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