Download the molecule 7jjg_B_VCD.sdf extracted from the PDB complex 7JJG

Download the bioisostere AD1058.sdf

Link to the original publication

Inputs:

Reference AD1058.sdf

Fragment to replace is number 2 in make_fgts_aggreg.sdf

Database pdb2

Results

In this tutorial, results show that the first molecule in ordered-bioisosteres-pdb2.sdf corresponds to the bioisostere 7jjg_B_VCD.sdf in the publication

Download best aligned bioisosteres ordered-bioisosteres-pdb2.sdf (162) and scores ordered-bioisosteres-pdb2-score.txt (more information on scores).

To visualize superimposition results: 3Dviewer

You can install and use DataWarrior (free software) to read the SDF file content as a table (available for Windows/Linux/MacOS-X)

Note: it has been observed that the minimization of some molecular structures is not sufficient with the standard process (RDKit, MMFF94 force field, 2000 Minimization cycles). This can sometimes cause some structure distortion).

Run completed

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To visualize results, you can use this webtool 3Dviewer and click to display superimposed bioisosteres

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