Can anyone suggest me free software or server like auto dock vina by which i can do molecular docking?

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Yoshinobu Ishikawa

Hi Nazmussakib,

I recommend idock:

https://github.com/HongjianLi/idock

https://github.com/HongjianLi/idock/releases/tag/v2.2.3

The docking procedure is almost the same as ADV.

Riaz A. Khan

Check PASS!

Md Nazmussakib Shuvo

Yoshinobu Ishikawa Thanks for your response. I will try ...

Mohadese Mohammadi

you can use PyRx

it's free and very easy to use.

Mohadese Mohammadi Thanks

Tehreem Tahir

Swissdock, a free web server. Moreover, yiu can get a 1 month free trial of Schrodinger glide package by asking them through proper channel.

Good luck!

Tehreem Tahir thanks

Bruna Soldera

Hey, Md Nazmussakib Shuvo I did not understand what exactly you are looking for, but the online software Mind the Graph has a service for subscribers that you can request a personalized illustration. Check their website. https://mindthegraph.com/

Hey Bruna Soldera I was looking for a free software by which i can dock ligand with my selected protein. I got some. If you know , you can also suggest me.

Thanks

Horacio Pérez-Sánchez

Achilles Blind Docking server at:

https://bio-hpc.ucam.edu/achilles/

In order to find more information and for discussion I suggest you to join the Structural Bioinformatics and High Performance Computing (BIO-HPC) discord server at:

https://discord.gg/fZyNYTsT7k

Horacio Pérez-Sánchez Thanks

https://anchor.fm/horacio-perez-sanchez/episodes/How-to-we-perform-computational-drug-discovery-I-Blind-docking-e1797tk

Saw Simeon

Hello Md Nazmussakib Shuvo

You can use SMINA (https://github.com/mwojcikowski/smina )or GNINA ( https://github.com/gnina/gnina ) docking tool for free. You may want to rescore the docked pose because the scores from docking tools are not very accurate (Article A Critical Assessment of Docking Programs and Scoring Functions

Ramchander Merugu

You can use Swissdock, Docking Server or Achilles blind docking server

Qifeng Bai

You can use MolAICal: https://molaical.github.io/MolDocking.html

Mosab Yahya Al-Nour

1. SwissDock online docking server: http://www.swissdock.ch/docking/view/swissdockd_MPI2lw_E80EQNJ2E6X16B2BFWF2

2. DockThor online docking server: http://www.swissdock.ch/docking/view/swissdockd_MPI2lw_E80EQNJ2E6X16B2BFWF2

3. MedusaDock online docking server: https://dokhlab.med.psu.edu/cpi/#/MedusaDock

Michael Weber

Just a few options:

SwissDock: http://www.swissdock.ch/

CmDock (a fork of RxDock which is based on rDock), even GPU-capability in development: https://gitlab.com/Jukic/cmdock

MTiAutoDock: https://bioserv.rpbs.univ-paris-diderot.fr/services/MTiOpenScreen/

Yogesh Sharma

Do you have experience with MTIopenscreen. how long does a job take?

Unfortunately, I can't say because so far I only used MTiAutoDock with a single ligand for each run (here, depending on the server queue, this takes approx. an hour).