Online cheminformatics

Content-type: text/html Online cheminformatics

Cheminformatic Tools and Databases for Pharmacology
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Scaffold-hopping using SENSAAS-Bioisostere

Inputs:

Reference molecule10.sdf

Fragment to replace is number 1 in make_fgts_aggreg.sdf

Database pdb

Results

In this tutorial, results show that the molecule number 173 in ordered-bioisosteres-pdb.sdf corresponds to the bioisostere Molecule 14 in the publication but with the 3 substituents of Molecule 10

Download best aligned bioisosteres ordered-bioisosteres-pdb.sdf (229) and scores ordered-bioisosteres-pdb-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