I need to find a solution to cluster a 100,000 compound library consisting of synthetic small molecules. Would I be correct to assume JKlustor can not handle a library of this size? Does anyone have any reccomendations for a solution which can handle this throughput? It would be much appreciated, thank you!
You can try Jarvis-Patrick (jarp) that can cope with this size even on an older HW. Sphere Exclusion can crunch 100K compounds in few minutes.
Depending on the diversity of the library to be clustered even LibraryMCS can be feasible (ie. if the input is less diverse, otherwise it runs really slowly).
Does this help?