Hello.

MarvinSketch allows you to save SDF files. It's from Chemaxon. However, they have a better tool that is JChem for Excel. It allows you to import chemical structures into a excel spreadsheet, maintaining dynamic links to the chemical formulae. I think it would fit you. It's not freeware, but you can easily get an academic license.

Best regards,

Ricardo Ferreira

Dear Ricardo Ferreira,

Thanks for your help.

I already tried with MarvinSketch but I cannot save several structures in a single file.

Indeed, when I created my database with MarvinSketch, I saved first each molecules separately with SDF file extension. Then I opened with notepad one of them and I introduced coords of the other one (copy and paste) as shown below:

Marvin 07311307482D

9 9 0 0 0 0 999 V2000

-1.1786 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.1786 -0.7072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 1.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

0.9648 0.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

1 6 2 0 0 0 0

2 3 2 0 0 0 0

3 4 1 0 0 0 0

4 5 2 0 0 0 0

5 6 1 0 0 0 0

6 7 1 0 0 0 0

7 8 2 0 0 0 0

7 9 1 0 0 0 0

M END

>

5.0

>

Example_1

$$$$

Marvin 07311307492D

10 10 0 0 0 0 999 V2000

-1.1786 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.1786 -0.7072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 1.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

0.9648 0.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

-1.1786 -1.5322 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

1 6 2 0 0 0 0

2 3 2 0 0 0 0

3 4 1 0 0 0 0

4 5 2 0 0 0 0

5 6 1 0 0 0 0

6 7 1 0 0 0 0

7 8 2 0 0 0 0

7 9 1 0 0 0 0

4 10 1 0 0 0 0

M END

>

6.5

>

Example_2

$$$$

Marvin 07311307492D

10 10 0 0 0 0 999 V2000

-1.1786 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.8930 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.1786 -0.7072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 -0.2947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-0.4641 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 0.9429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.2504 1.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

0.9648 0.5304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.1786 -1.5322 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

1 6 2 0 0 0 0

2 3 2 0 0 0 0

3 4 1 0 0 0 0

4 5 2 0 0 0 0

5 6 1 0 0 0 0

6 7 1 0 0 0 0

7 8 2 0 0 0 0

7 9 1 0 0 0 0

4 10 1 0 0 0 0

M END

>

4.5

>

Example_3

$$$$

This is an example with 3 molecules (Example_1, Example_2 and Example_3) and with pIC50 of 5.0, 6.5 and 4.5, respectively.

Now, to introduce biological values and/or names I put a small "script" as below:

>

4.5

>

Example_3

I think for small library this procedure would be OK but not for big one.

So, I will try with your second suggestion with JChem which seems to be better ;-)

Best regards,

Enrico

You could use InstantJChem from ChemAxon. I think it´s also free like Marvinsketch. It´s a quite good chemical database. You can put in and connect almost every data you need and you can also export your data as sdf.

Dear Daniel Ramsbeck,

I just finished to download and install the software.

I will try to create a database.

Thanks for your help.

Best regards,

Enrico

@EP. One can develop a chemical database using public domain software tools, available in plenty. One of them i used to develop a chemical database of the compounds synthesised at CDRI. If you want I can help you. It is all very easy. once you develop the database then you can think of a number of alternates......

Dear Egon Willighagen,

Thanks for your help.

Best regards

Dear Prof. Ravi Sharma,

Thanks for your help. With your chemical database, can you find a molecule by structure search?

Best regards

I also would use InstantJChem from ChemAxon. This Java based tool is one of the best database tools for handling chemical structures, including im- and export and substructure search, as well as the organization of meta data (inhibition constants etc.) You should take a look if it is really free, but for a test system I would start with it.

@EP:

Perhaps you know "how the structure search is conducted internally in a software process"?

for searching generally:

1. the structure is converted in SINGLE line representation. then you can devise string similarity search to arrive at % of similarity between sample structure and the records (structure) in the database

2. Here your structure remains an an image and you match images

3. Searching structure through key words: allocate key words to structures in your database, the on the basis of key words match, hits of structural images can be displayed

Dear Prof.Ravi sharma

How can use the EP? what is the address?

Thanks

@SM ---> (SAMEERA)

@EP is not any software but i wanted to say that my comments are for the author of the thread "Enrico P".

well one of the softwares available free is epi-info developed by WHO for epidemiological studies. using this software i developed 8 databases. very easy to learn. there are two versions 1. dos 2 windows. both are good but i liked dos version very much. pl tell

I will suggest to visit following sites for free software for drug design

http://osddlinux.osdd.net/

http://crdd.osdd.net/

http://www.imtech.res.in/raghava/

You can use

http://merian.pch.univie.ac.at/pch/download/chemistry/moldb/moldb5r.tar.gz

for creating this datbase without any cost