Autodock is the best software for molecular docking

You can try Autodock and/or VINA for docking and USCF Chimera for QSAR.

To download, go to the webpage:

http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/

First , you should download mgltools ,then you can use autodock easily

http://mgltools.scripps.edu/downloads

Autodock is best free software for docking/virtual screening. But QSAR is not only docking, so what exactly you are looking for QSAR?

You can use following software for QSAR study

Discovery studio or

Tripos sybyl software http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=SYBYL-X or Vlife MDS http://www.vlifesciences.com/products/VLifeMDS/VLifeQSAR.php

@ Nitish Mishra: Actually I am interested in both QSAR and Docking. First, to generate QSAR models. Then, evaluate the model by docking results using 2D interaction diagram.

Sybol is better than Scridinger

COMFA and COMSIA models by sybyl

if you are using metalloproteins it is better to use QPLD in schrodinger suite

for docking you have many options : Autodock is the best I think as it has versatile way of performing your experiments and it can utilize various docking algorithms.

also you can use Dock which is a freeware from UCSF

QSAR can be done using any statistical software if you have the descriptors calculated ... you will need a software to calculate the descriptors of your compounds

Accelry's discovery studio has some options to select the descriptors in an automated fashion using GFA.

Both of Accelry's and Sybyl products are not free wares and they need licence for thier usage

for 3D QSAR ........ you may use Open 3D QSAR if you want a freeware as CoMFA and CoMSIA are not free

Good luck

I suggest u to go for molegro Virtual Docking software (Renee thompson) which is easy and user friendly for docking various ligands and protein I have used this software for my inhibitory compounds and get data well u can get a free licensed evaluated copy with fully activated features

Hi,

You can use LQTAgrid (4D-QSAR) freely available (http://lqta.iqm.unicamp.br/portugues/siteLQTA/LQTAgrid.html).

And yeah, Autodock is the best freely available docking software. If you face problem in using Autodock command line then try autodockvina plugin in PyMol (again freely available). And of course, you will need MGL Tools installed in your computer prior to using PyMol plugin for autodock.

Happy docking.

Nutan

From my experience, I recommend to use MOE (Molecular Operative Environemnt), which is a complete package of chemoinformatics and bio-informatics. With that, you can not only run docking, but also perform QSAR. Moreover, with docking approach, and with the new version of MOE 2012, including the Amber12: EHT force-field, for a given pose, you can easily perform minimization in order to obtain accurate dG.

Other software which could be extremely useful is AutoDock Vina, which is free for academia, and for QSAR, as the result will extremely rely on the previous alignment, I recommend any software you can download, because having expermiental data about your ligands, all them predict very consistent and compatible outcomes.

if you aware of statistics ,you can use Weka for QSAR

Accelrys (Discovery Studio) provides a commercially industry validated software. Perhaps you could try that as well.

Hi,

Please visit: http://open3dqsar.sourceforge.net/ for freeware but it is not really easy to use it... but you can try.

Of course some others better softwares are available (but not free): Molecular Operating Environment (MOE) where you can find a lot of helpful tutorials, SYBYL software and as Mai Chun Wai recommended the Discovery software.

Best regards,

EP

Yup agreed to Enrico Perspicace =)

Concerning free softwares I think Autodock/ADT (MGLtools) is the best choice. If you have money to spend, I agree with others here suggestin Sybyl package. However, the best poses are those furnished by GOLD (CCDC)

I have free online service http://www.vls3d.com/links.html, please if any one use one of these, could he tell us about it

material studio would be an option in conjuction to the accelyrs' Discovery studio

http://www.youtube.com/watch?v=RuKa6m7AJZw demo on sybyl for fragmentation

Concerning free softwares for Docking in my view Autodock/ADT (MGLtools) is the best choice. For descriptor calculation- PaDEL-Descriptor - NUS - National University of Singapore is the best option.

For QSAR analysis you can try to use Virtual Computational Chemistry Laboratory http://www.vcclab.org/lab. It is free, is a server that you can generate some QSAR models and generate DRAGON descriptors.

Sorry for the late reply.

I do hope you have got idea now for docking.

You can try McQSAR from Abo Akademio Univerity, Finland

In my experience, Autodock (mgltools) with combination of vina is the most fast for doing docks [O. Trott, A. J. Olson, “AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading”, Journal of Comp. Chemistry, vol.31, pp. 455-461, 2010]

Dear,

Auto dock is only useful when you plan to dock a ligand to a receptor not protein to a protein. I have a brief guide for your plan to select the best software:

For Docking study included energy minimization and protein optimization (Ranked by my experience) (All of these softwares are capable of perform a diverse format of docking simulations):

1- ICM-Pro

2- Schrodinger

3- Discovery Studio

4- MOE

For image preparation:

1- ICM-Pro

2- Schrodinger

3- MOE

4- Discovery Studio

For protein visualization:

1-ICM-Pro

2- Schrodinger

3- MOE

4- Discovery Studio

For QSAR analysis:

1- Discovery Studio

2- Schrodinger (canvas)

3- ICM-Pro

4- MOE

Although all of these softwares are commercial, but you can find them for free if you do a little search.

Bests,

for QSAR use sybyl, for docking, try Gold, Glide and Autodock

You can use Autodock for molecular docking if you want to dock multiple ligand to one protein than you use my folwchart for it. For QSAR you can use KNIME and CDK tools which free. my email id is [email protected] feel free to write to me

Scigress explorer in one reliable software for QSAR and docking but it is a paid one. Also, you may try Autodock vina whose predictions are very good.

Audock is the best free software for docking studies. For QSAR studies you can use CDK tools, QSARpro: its a paid software but you can obtain a free license

I think, Autodock Packages (Autodock 4.2/Vina) are one of the best software for docking studies. It is one of the highly cited package.

I think Flex X/Discovery Studio is one of the best software for Pharmacophore as well as QSAR studies.

Regarding free software, JChem from ChemAxon might be a good tool for QSAR studies.

The link is http://www.chemaxon.com/jchem/intro/index.html

Regarding free software for docking, AutoDock is he best one. The more preffered will be AutoDock Vina owing to its accuracy for docking calculations.

AutoDock Vina and PRECLAV ARE GOOD Software.

Which freely available softwares results can be used in publishing the papers?

Like I have seen the results of the Autodock can be used in publishing the papers.

Autodock will be always the best free software for getting accurate interaction profile between the ligand and the protein.

Http://vina.scripps.edu/download.html to download vina

http://vina.scripps.edu/manual.html its manual if you need more help in doing automated docking mail your query at [email protected] i will send you scripts which you can run at your system to do automated docking using vina

Sameer Chaudhary,

Please let me know the exact procedure to run docking in vina. I am poor in using the vina. please let me know th installtion procedure. in chaich i have to insall the vina as per your consideration.

Currently i am using the windows server 2008 with RAM of 16GB..

Please help to do the same.

hi Sameer i am working on autodock and want to work with autodock vina so can you please help to get the scripts as you said. thanks in advance

my mail id is [email protected]

NUTAN CHAUHAN:

HEY DEAR.........

i am working on 3d qsar through sybyl..

u shared a link bt dts not opening is there any other free software for 4D QSAR??

or any other free online software for 3D QSAR???

send me details on my mail ID : [email protected]

thanking you..

Dear Dhara Chhatbar,

This is the only link where you can access the software. Try copying the link and paste in new tab. It should work.

Regards,

Nutan

Dear all, I have tried to download Sybyl-X which requires a license, please to send me academic license If you have, Thanks in advance.

my email adresse: [email protected]

SyByl software is more efficient for all QSAR studies.

but Sybyl-X is not free, can you give me a free software for QSAR?

How can we do molecular docking with number of ligands and one protein structure. For this which software is more accurate?

Dear friend,

It is very difficult to define what is "best" as each software depends on the docking protocol and scoring method. The performance of these strongly depends on the nature of the receptor site and the ligand.

Regards

Dear friend,

QSAR Tool box Software is best for QSAR Studies and AutoDock Vina is best for Docking studies.

In my experience it works with Ubuntu 12 -14 LTS

please check the Link with drug propeties predicion 

Molecular Properties Prediction - Osiris Property Explorer

It provides good QSAR properties analysis 

Molecular Properties Prediction - Osiris Property Explorer

www.organic-chemistry.org/prog/peo/

For QSAR model development, you should try the freely available tools at DTC lab website (attached link)

http://dtclab.webs.com/software-tools

for multiple ligands docking the best choice is vina autodock with the freely available discovery studio viewer 4.1 

thanks

You may want to have a look at EasyQSAR available at http://easyqsar.blogspot.in/

Hi Nutan ! Do you have other link to LQTAgrid?

Please refer various tool at Directory of computer-aided Drug Design tools (https://www.click2drug.org/ ). Interestingly most of the tools are free.

Hello I dont use QSAR,

Best regard

Hello

CASTp, Autodock vina, Swissmodel, Chimera, Qsite and BIOVIA Discovery Studio.

Check in these links. It might help you.

https://www.click2drug.org/

Good Luck.

http://crdd.osdd.net/qsar.php

You can check Alvascience tools for chemoinformatics and QSAR:

https://bit.ly/37pyzJq

Try POLLY and Triplet software for descriptor calculation.

QSARINS is also free software for studying 2D-QSAR study. It is based on multiple linear regression and Genetic Algorithm. In this software, you can get following fitting, internal and external validation parameters:

• Fitting Parameters: R2, R2adj, R2-R2adj, LOF, RMSEtr, MAEtr, RSStr, CCCtr, s, F
• Internal validation Parameters: Q2loo, R2-Q2loo, RMSEcv, MAEcv, PRESScv, CCCcv, Q2LMO, R2Yscr, Q2Yscr
• External validation parameters: RMSEext, MAEext, PRESSext, R2ext, Q2F1, Q2F2, Q2F3, CCCext

You can get predicted vs experimental activity plot, residual plot, Applicability domain as well as Y-scrambling plot easily from this software for given in the figure section of the manuscript.

You can download this software from the following link:

http://www.qsar.it/

First of all, you must go through a registration process by putting in your academic email id or also giving a solid reason to fulfill all the criteria to download this software. One interesting part of this software is that the Padel software will also automatically download, which gives a chance for molecular descriptor calculation.

The tutorial video of it is available on YouTube:

https://www.youtube.com/watch?v=G9dvzzLTE60

I suggest AutoDock and AUtoDck Vina for Molecular Docking. Based on my experience, these two are the best softwraes for molecular docking. For QSAR docking you can use, QSARINS and FlexX

See this

https://www.youtube.com/watch?v=BX80RYr1f08

For regression and classification-based QSAR modeling, one can go for DTC-QSAR Software (with a user-friendly GUI) freely available to download here: http://teqip.jdvu.ac.in/QSAR_Tools/

More details are in the flyer (attached).

Have a Look at Online chemical database

(https://www.alvascience.com/)

Have a lot of software can do the same results