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Can you tell me a little about Schrodinger's approach to fragment based screening? Is there a fragment library that I could access?

We have several scripts that can be used for for working with fragments, available from the Scripts menu in Maestro. For example, the "Combine Fragments" GUI can be used to generate new compounds from pre-positioned fragments that make favorable interactions with a target. These fragments could come from crystal structures of bound ligands, or from docking fragments with Glide.

If you dock fragments with Glide, using Maestro to set up and run the job, we recommend changing some of the Advanced Settings on the Settings tab:

  • Increase the initial number of poses per ligand kept from 5000 to 50000;
  • Widen the scoring window from 100.0 to 500.0;
  • Increase the number of minimized poses per ligand to 1000;
  • Select "Use expanded sampling".

These parameter changes widen the docking funnel, which we've found helpful when docking fragments.

We offer a prepared fragment library on our web site. The Glide fragment library is available for download here. This library can be used for fragment docking, core hopping, lead optimization, etc.

One way to use the fragments is with CombiGlide, which is a combinatorial screening tool. With a common core and reagent libraries that could be attached at one or more points on the core, CombiGlide performs rapid screening of the combinatorial space without requiring the docking of every member of what could be an enormous combinatorial library. A diverse side-chain collection is available on our web site here.

You can also use the Core Hopping product, in which the core varies rather than the side chains. A library of cores is available in the software distribution. It appears in the file selector when you import a core file, as Schrodinger Cores. (You might need to widen the file selector list to see the full name.)

Keywords: fragment library, fragment based screening, CombiGlide

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