ADL: High Troughput Docking by AUTODOCK and/or VINA

Amr ALHOSSARY amr_alhossary at hotmail.com
Tue May 12 03:00:16 PDT 2020


Hi Cristina,

1) Instead of Vina, you can use QuickVina 2. It is MUCH faster than AutoDock Vina.
2) You can perform Blind docking over the whole receptor search space using QuickVina-W.

Both can be found from https://qvina.github.io/

Best of luck.

Regards

Amr


Dr Amr Ali Mokhtar ALHOSSARY
Research Fellow, Biomedical Informatics Lab, School of Computer Science and Engineering
50 Nanyang Avenue, NS4-04-33, Singapore 639798
T +65-9457-2816 F +65-6791-9414 aalhossary at ntu.edu.sg www.ntu.edu.sg


-----Original Message-----
From: autodock-bounces at scripps.edu <autodock-bounces at scripps.edu> On Behalf Of cristina tomasella
Sent: Wednesday, May 13, 2020 1:27 AM
To: autodock at scripps.edu
Subject: ADL: High Troughput Docking by AUTODOCK and/or VINA

To Whom it concerns:

Dear Mrs/Mr,
 the research group in which I work  is part of a network to find new potential anti-COVID 19. I have  to carry out a  docking of hundreds of compounds from a database in several possible binding sites . 
Docking each molecule alone in each binding site might be very difficolt and make confusion. Is it possible some way to speed up (docking all together of the ligands and possibly into all the binding sites) the docking calculations by AUTODOCK and AUTODOCK VINA ?
Thanks in advance for any your consideration and support .
Best regards,
Cristina Tomasella
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