ISIS/Draw MOL Format

ISIS/Draw is a free molecule-drawing software contributed by MDL Inforamtion System, Inc. and 3DFS accepts the MOL format output of ISIS/Draw as the 2D substructure searching query input.

First, draw your query substructure which can be a molecule or  fragments (less than 7) in ISIS/Draw, then export it as MOL format. The only thing you should be take care of  is about hydrogen atoms.  Explicitly draw the bond connecting a hydrogen if you expect the hits with the same number of hydrogens as the query.

For example: Both 1 and  2  are hits of Query 1, however, only 2 is the hit of Query 2.

            Query 1                                                      Query 2
                    

                    1                                                                2

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