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Advice on Molecular Similarity by Shape akin to ROCS?
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Rudy

Joined: 18 Dec 2009
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Link to postPosted: Sun May 24, 2015 11:05 pmPost subject: Advice on Molecular Similarity by Shape akin to ROCS? Reply with quote

Hello,

Could you please give me advice on which ChemAxon products to use for shape matching of molecules, e.g., by a shape-based Tanimoto coefficient?

Related to this, which of the ChemAxon products would be comparable to OpenEye shape matching and screening software such as ROCS or Fast ROCS?

Has anyone done a comparative review of ChemAxon and OpenEye software in this regard?

Thank you.

Best regards,

Rudy

 

 

 

 

 

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Tue May 26, 2015 2:03 pmPost subject: Reply with quote

Dear Rudy, 

We have a tool called Screen3D which is for 3D shape based virtual screening and similarity search. This tool is based on our 3D Alignment Plugin/Module, which performs alignment for molecule pairs based on molecular shape. 

You can find our manual page and the reference publication below. The publication contains description of our screening method and also benchmark results.

https://docs.chemaxon.com/display/screen/Screen3D

I hope this helps. 

Daniel

Rudy

Joined: 18 Dec 2009
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Link to postPosted: Tue May 26, 2015 2:21 pmPost subject: Screen3D and Tanimoto Reply with quote

danielszisz wrote:

Dear Rudy, 

We have a tool called Screen3D which is for 3D shape based virtual screening and similarity search. This tool is based on our 3D Alignment Plugin/Module, which performs alignment for molecule pairs based on molecular shape. 

You can find our manual page and the reference publication below. The publication contains description of our screening method and also benchmark results.

https://docs.chemaxon.com/display/screen/Screen3D

I hope this helps. 

Daniel

Dear Daniel,

Thank you for your reply. This is quite helpful.

I am also looking for ways to compare molecules with respect to their shape and to output the Tanimoto coefficient as an index of this similarity. Are there any ChemAxon products that will output the Tanimoto coefficient?

-- Rudy

 

 

Daniel
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Link to postPosted: Tue May 26, 2015 2:54 pmPost subject: Reply with quote

Hi, 

Yes, the screen3d command line tool ouputs 3D shape Tanimoto similarities for similarity searches. So you can compare molecule pairs with it using the 3D Shape Tanimoto similarity. It also prints these values to the output.

Daniel

Rudy

Joined: 18 Dec 2009
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Link to postPosted: Tue May 26, 2015 3:02 pmPost subject: Screeh3D Tanimoto Reply with quote

danielszisz wrote:

Hi, 

Yes, the screen3d command line tool ouputs 3D shape Tanimoto similarities for similarity searches. So you can compare molecule pairs with it using the 3D Shape Tanimoto similarity. It also prints these values to the output.

Daniel

Hi Daniel,

Excellent! I am eager to learn how to use Screen3D. I am in the process of applying for a renewal of my academic research and teaching licenses for ChemAxon products.

Best regards,

Rudy

 

Daniel
ChemAxon personnel
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Link to postPosted: Tue May 26, 2015 3:58 pmPost subject: Reply with quote

Hi, 

Well, screen3d is quite easy to use as it is a command line tool. If you download it, type screen3d -h to get the full help manual with examples. Also you can use the manual I linked above to get working examples for screen3d. 

Daniel

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