QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: GJK on October 25, 2013, 19:34

Title: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: GJK on October 25, 2013, 19:34

Dear all,

We have licensed ATK system in our Department (Physics & Nanotechnology-SRM University-INDIA-CHENNAI-KATTANKULATHUR).I am working on graphene based structures related to cancer therapy.We have drugs in our database (Version 12.8) but there is no availability of anticancer drugs & cell line structures(normal & cancerous cell lines).I am are very eager to implement those structures in my research.Kindly do the needful.

Thank you
Jananikumar

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: Anders Blom on October 26, 2013, 06:51

You can import structures in e.g. XYZ format into VNL.

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: GJK on October 29, 2013, 11:40

Dear sir/mam,

From where can we export the XYZ file format database files and the anticancer drug structure.
Also we do not have any special .xyz files.
I will be highly grateful if I am being provided with  data base of anticancer drugs. Kindly do the needful.

Thanks & Regards
Jananikumar

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: Shinji Usui on November 1, 2013, 02:41

There are several drug databases.
http://www.drugbank.ca/
http://www.genome.jp/kegg/drug/

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: GJK on November 5, 2013, 17:33

I require your help in knowing the procedure to download the drug structure as .xyz format compatible with the licensed software.
I have seen the drug bank as open source data base.If you could provide  how to download one drug structure ( for example) then it will be easy for me to download the drug structure files.

Thank you
Janani.K

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: Shinji Usui on November 6, 2013, 02:06

Dear GJK

I think you can download structures as a Mol format and
use openbabel (http://openbabel.org/wiki/Main_Page) to convert it to XYZ format.

BR
Shinji

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: GJK on December 18, 2013, 12:59

First of all I convey my sincere thanks to all supporters of ATK. I request your help for the file conversion where I am facing problems.

1. I can save the mol file format only as txt after opening from the drug bank,while giving the save as option .Just help me how to save in mol format.
2.I lack the procedure to convert it to .xyz files using open babel.Kindly help me in sorting out this problem? so that I can start my research.
3.Even though I tried for file conversion using open babel I could not save the output file.Kindly also specify the destination folder.

Regards
Jananikumar

Title: Re: Requirement of anticancer drugs and cell lines(normal & cancer) in the data base
Post by: Shinji Usui on December 19, 2013, 01:50

Dear GJK

1. I can save the mol file format only as txt after opening from the drug bank,while giving the save as option .Just help me how to save in mol format.
Right click on the mol character part in the web and save it.  

2.I lack the procedure to convert it to .xyz files using open babel.Kindly help me in sorting out this problem? so that I can start my research.
See. http://quantumwise.com/forum/index.php?topic=2543.msg11886#msg11886
and http://openbabel.org/wiki/Babel

3.Even though I tried for file conversion using open babel I could not save the output file.Kindly also specify the destination folder.
I think you can get a saved xyz file by procedure 2.

BR