By Dr Neil Taylor
When it comes to enterprise software pricing, the debate between site licenses and per-seat licenses reveals fundamentally different philosophies about value and access.
Per-seat licensing says: “You pay for each individual who uses the software.”
Site licensing says: “You pay for unlimited access within your organisation.”
For research-intensive fields like drug discovery site licensing offers compelling advantages. Let’s examine where per-seat and site licensing differ in the context of software and protein structure databases in the fields of drug discovery, molecular dynamics and computational chemistry.
Key to success in these fields is access to data, open and transparent workflows and scientific collaboration, and the choice of licensing model can have an unexpected impact.
| Feature | Per-seat licensing | Site licensing |
|---|---|---|
| Cost basis | Headcount ($10k/user/year x 20 users = $200,000/year) | Predictable, flat annual fee ($250k) |
| Access | Restricted (gatekeepers) | Universal (everyone) |
| Admin | High (tracking/audits) | No tracking individual users |
| Growth | Costs scale with headcount | Encouraged by scale |
The difference isn’t just arithmetic, it’s philosophical.
Under per-seat licensing, a medicinal chemist who wants to check protein ligand binding predictions must either ask a computational chemist to run the analysis or wait for a new license to be approved. Under site licensing, they simply log in and run it themselves. Faster iteration, better decisions, more integrated workflows. Few things frustrate drug hunters more than being unable to begin their work because no software license tokens are available.
Site licensing turns software from a rationed resource into shared infrastructure.
Per-seat models require constant tracking: provisioning new users, deprovisioning departing employees, managing access tiers, running compliance audits. One pharmaceutical company estimated needing 0.5 FTE IT support to handle tickets associated with seat-based license tokens for research software
Site licensing eliminates almost all of this -everyone gets access.
Some of the best insights come from unexpected sources – the crystallographer who notices something unusual, the pharmacologist who spots a pattern, the project manager who runs an analysis while preparing a report, the visiting consultant who is asked to take a quick look at some edge case results.
Per-seat licensing creates a barrier: “Is this person’s occasional use worth $10,000/year?”
Site licensing enables serendipity. When anyone can use the tools, you’ll routinely get access to cross-functional insights, different ways of seeing, faster hypothesis testing, and democratised expertise.
With per-seat licensing, hiring 5 scientists automatically increases your software budget by $50,000. CFOs start seeing licenses as a tax on growth. Site licensing gives you a fixed annual cost independent of team size, allowing you to budget accurately years in advance and grow without automatic software cost increases.
A 100-person biotech running 10 drug discovery programs gets more value from structural biology software than a 20-person company running 2 programs. This isn’t because they have more users, but because they’re operating at a larger scale. Site licensing recognises this. Pricing scales with organisational capacity and value extraction, not with the arbitrary metric of user count.
The site license vs. per-seat debate ultimately comes down to how you conceptualise the software:
A protein structure database isn’t just a tool for computational chemists, it’s infrastructure for drug discovery. Infrastructure should be universally accessible, predictably priced, and free from artificial scarcity.
Per-seat licensing optimises for vendor revenue growth through user count expansion.
Site licensing optimises for customer value by removing access friction, enabling collaboration, and aligning costs with organisational scale rather than headcount.
Yes, site licensing often appears to cost more on paper. But when you factor in administrative overhead, lost productivity from access friction, and missed opportunities from limiting access, there is a hidden opportunity cost that shouldn’t be ignored. With longer term thinking, the total cost of ownership typically favours site licensing for research and innovation-focused organisations.
The question isn’t just “How much does it cost?” but “How does the pricing model affect how we work, collaborate, and create value?” That’s why this is as much an economic question as a cultural one.
This philosophy isn’t new. At DesertSci, we’ve offered site-based licensing for over 25 years because we fundamentally believe in focusing on innovative outcomes for drug discovery and computational chemistry, not just overheads. In our experience, it has always been the case that more eyes looking means more is seen, and this is critical to success in drug research, discovery and development.
When your mission is enabling successful drug discovery, the last thing you want is unnecessary barriers preventing all members of all your teams from accessing the data they need to succeed. We’ve seen firsthand how removing access friction accelerates innovation and leads to better science and more successful candidate discoveries. Site licensing isn’t just a pricing model for us; it’s a reflection of our commitment to our customers’ success.
For more insights on optimising drug discovery workflows and managing enterprise protein data, follow Dr Neil Taylor on LinkedIn. Or, if you’d like to arrange a demonstration of DesertSci’s Proasis, please get in touch with our team.
