[Dock-fans] Need some help with my dataset

Trent E. Balius tbalius at aol.com
Fri Aug 11 09:03:34 PDT 2017



 Hi Ribas,

You might want to use the footprint scoring function to calculate hbonds and strong residue interactions:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#FootprintScore

see this tutorial for how to run footprint score:
http://ringo.ams.sunysb.edu/index.php/2017_DOCK_tutorial_1_with_PDB_4QMZ_NEW#Minimization

If you use your favorite text editor to open the mol2 dock output, you will see that the values in the viewdock window is also in the mol2 file.  Chimera also allows you to compute h-bonds and display these in the viewdock window.  you will need to calculate these a different way.  Footprint score does calculate h-bonds.  

You can grab these values from the mol2 file and put them in a new file as I suggested. 

I hope that this helps,

Trent  

 

======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: José Ribamar dos Santos Ferreira Júnior <zeribajr at usp.br>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Aug 10, 2017 3:49 pm
Subject: Re: [Dock-fans] Need some help with my dataset



Dear Trent,


thanks for helping. Would that also be feasible with the "number of hydrogen bonds", and "residues interacting with the receptor" for each small molecule she docked?


Usually I need to open the mol2 file in Chimera and inspect for that visually, then fill up the excel plan, and it seems there is no way to extract it from any file format. Do you know any solution for this problem?


Thanks again for your help. 


All of the best


Ribas



On Thu, Aug 10, 2017 at 7:22 PM, Trent E. Balius <tbalius at aol.com> wrote:

 Hi Ribas,

I would suggest writing a python (or your favorite computer language) script to do this.

Have it read in the mol2 file and write out a csv file.
  
All of the information in viewdock is in the mol2 file.  

You could even do this with grep, awk, and paste.

Do something like this:

>> grep "######    Name:"  mol.mol2  | awk '{print $3}' > name.txt
>> grep "######    GridScore:" mol.mol2 | awk '{print #3' > score.txt

 >> grep "######    Int_energy:" mol.mol2 | awk '{print #3' > int_en.txt

 
>> paste -d, name.txt score.txt int_en.txt > file.csv

I did not check that this works.

Then open this csv in Excel. 

I hope that this helps,

Trent



======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 


-----Original Message-----
From: José Ribamar dos Santos Ferreira Júnior <zeribajr at usp.br>
To: dock-fans <dock-fans at docking.org>
Sent: Thu, Aug 10, 2017 1:18 pm
Subject: [Dock-fans] Need some help with my dataset



Hi,


I have a colleague with whom I work, she did some docking simulations with several molecules and showed me the results in Chimera (https://www.cgl.ucsf.edu/chimera/). She later asked me to transport to an excel plan the data from about 400.000 molecules docked. I´m doing this by hand and sent an email to Chimera developers that told me there is no way to transport this information directly to an excel file. Could someone, please, help me with this problem? Does DOCK has a way to put molecules information directly into a worksheet. The information I need is molecule name; Grid Score;  Int_energy; number of hydrogen bonds, and residues interacting with the receptor. Thank you in advance.


Ribas




-- 

José Ribamar dos Santos Ferreira Júnior
Universidade de São Paulo
Escola de Artes, Ciências e Humanidades
Laboratório de Biotecnologia
Av. Arlindo Béttio, 1000 - Ermelino Matarazzo
Bloco A3, piso térreo, Ala 2
São Paulo - SP
CEP 03828-000
Fone: 11-3091-8873




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-- 

José Ribamar dos Santos Ferreira Júnior
Universidade de São Paulo
Escola de Artes, Ciências e Humanidades
Laboratório de Biotecnologia
Av. Arlindo Béttio, 1000 - Ermelino Matarazzo
Bloco A3, piso térreo, Ala 2
São Paulo - SP
CEP 03828-000
Fone: 11-3091-8873




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