Hi all,

I got a problem with similarity search using ECFP4 with Tanimoto similarity score. I`m performing a similarity search on a database with the attacched protocol n. 00260329.xml. I have to perform a VS using multiple queries (217 in total). I need to oobtain in this way a similarity tanimoto matrix composed in this way:

                    query01     query02     query03      ....     ....

mol_1           0.87            0.98         0.23

mol_2           0.45            0.56         0.85

mol_3           0.78            0.78         0.89

...

....

....

...

and so on....

The important thing I need to retain is the exact ordering of the query structure. That`s the problem I have with the attacched  PipelinePilot protocol. The attacched protocol is able to calculate every Tanimoto similarity for each candidate and vs each query but then, in the output files candidates are ranked from the top to the bottom of Tanimoto score. Instead, I need to retain the exact ordering of the queries structures without any ordering. I try to exclude the N-filter component from the protocol as well but it doesn`t change a thing.

Does anyone know a solution to this problem? I attacch to this message the xml input file obtained with the uncorrect top/bottom ordering  that I wouldn`t have.

If I wasn`t clear, please ask....

Thanks for the suggestions and helps

Francesco