Many early stage companies may be missing out on the value that docking can provide at the validated hit and hit-to-lead stages of development, where structure/activity relationships (SAR) can help guide chemistry development of lead compounds.
While docking large HTS libraries with millions of compounds may require specialized CPU clusters, docking of small libraries (i.e., thousands of compounds) and SAR compounds from experimental assays is readily achievable in short time frames with a relatively inexpensive Intel Xeon workstation.
Following an initial investment in the workstation and software, follow-on costs are minimal (e.g., electricity, IT support and data backup). Turnaround times may be faster than with CRO services. Also, sensitive IP data is also protected by being retained onsite and not transmitted over the internet.
Equipment / cost breakdown:
Software:
AutoDock Vina (non-restrictive commercial license) cost: free
Accurate (benchmarked against 6 other commercial docking programs)
Compatible with AutoDock tools
Optimized for speed (orders of magnitude faster than previous generation)
Parallelized code for multi-core systems
AutoDock Tools (non-restrictive commercial license) cost: free
PyMol Incentive (commercial license) cost ~$90 / mo
Visualize docking results, free plugin can allow Vina to be run within PyMol GUI
Fedora Linux cost: free
Hardware:
HP Z620 Workstation (stock configuration) cost: $2999
2 GHz (6 Core) Intel Xeon E5-2620 2GHz
USB keyboard and mouse cost: $50
Dell Ultrasharp 27” LED monitor cost: $649
1TB USB HD for data backup cost: $150
IT support for initial setup ~ 4 hours cost: $400
Total initial capital expenditure: ~$4350