I find Cresset Spark with their databases very useful for generating a library of ligands with common templet. But it is a commercial software and its evaluation can be requested.
Hi Paddy, I prefer zinc database. These compounds are available for purchase. You can also try Maybridge or bindingdb.org.. These have Ki or IC50 values as well. Hope it helps :)
Pipeline Pilot (3dsbiovia.com) can generate libraries from two or more fragment sets. The generated compounds can then be converted into docking-ready energy-minimized 3d structures.
There are many programs that can automatically generate virtual libraries, but one should be careful as they might produce synthetically not feasible solutions. I think it is reasonable to ask experienced chemist to check the library or use chemist-supervised semi-automatic approach if you have such option. It would also make sense to filter compounds with required substructure from databases of published compounds at least to get some ideas what was already synthesized. Some databases (e.g. Reaxys) allow to download the found structures as sdf file. Finally, it is getting popular to screen pre-generated virtual libraries provided by vendors, e.g. Real database from Enamine. They are much bigger than databases with published or synthesized compounds, entries have defined prices and are claimed to be available in a reasonable time with high probability.
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