Please read my recent publication.

@Sergey Shityakov 

Sir,

I'm asking a general question... Molecular Docking uses very simplified force field and their results may often be inaccurate..... What is, in your experience, the average accuracy of Docking results in drug-protein or drug-DNA or protein-protein type of interaction...?

Dear Qaiser,

tough question that you are asking here. As you mention, the binding affinities reported by Vina are only predictive and rely on an energy function somewhat empirical. Vina is definitely valuable for predicting a binding mode of a small ligand, but ranking two bound models is really up to the user appreciation. It usually can not be trusted on its own and requires some sort of cross-validation. One rule of thumb is to consider models with binding affinity lower than -6 kcal/mol. One way might be to take a bunch of random structures and dock your ligand of interest. Then try to fit your results into a normal distribution and calculate the probabilities of your two initial models to be sampled ( a sort of p-value if you will). This is what I would do, off the top of my head.

Short answer: In view of the errors typically associated with ligand docking, I'd say that the 2kcal/mol that you mention above are not a conclusive difference.

Long answer: As discussed by Julien, the scoring functions from docking program are essentially optimized for predicting the binding mode. To that, you need to add all the potential pitfalls in handling the receptor (flexibility,...). So, I'm always doubtful about predicted affinities. And it would take some work for convincing me that a difference is significant...

1) For a training set containing ligands for protein A, try to correlate your docking scores and your activities. Your ligand should normally be comparable to the molecules used in the training set. Is your R² OK? What is your RMSE for affinity prediction, based on docking score?  If you cannot get a correlation with affinity, how would you trust that a difference is significant?

2) Do the same for protein B.:-)

3) If you succeed in having a good correlation for the two targets, and that the difference between the two predicted affinities is superior to the combined RMSEs, then, I'll be willing to consider that the difference is significant.

And obtaining that is far from trivial...

hi Julien Jorda .. Can you please provide some reference regarding the thumb rule for considering the actives as

@Julie Jordan,

Using auto dock vina, RNa aptamer which was experimentally binding with Target 1 were possessing same binding affinity towards the target 2 while docking . Then how come we validate the specificity of the RNA aptamer using these softwares?

Dear Qaiser Fatmi

If your drug binds to two different proteins with different BE values, I believe the best approach is to determine if this difference is important using real experimental techniques. If your drug can inhibit (or activate) these proteins at the same time, this would mean that the difference of 2 kcal/mol between the BE values is not important; however, if your drug can only inhibit (or activate) one protein but not the other one, it would mean that the difference of 2 kcal/mol is important.

I hope this answer will help you.

What kind of difference in the docking score between a peptide ligand and its receptor is considered to be significant? If the scrambled peptide is scoring -40 kcal/mol vs the experimental peptides scoring a range between -60 to -75, would this be considered significant? Thanks in advance.

Can anyone help me my docking score is -7.4 weather it is good score

http://journal.umpalangkaraya.ac.id/index.php/jmd/announcement/view/17

https://docs.google.com/forms/d/e/1FAIpQLSfNpiah9wUc--jA7V1_42J2M3Cjlgtvgj-vDEasBIPXbEs9MQ/viewform?usp=pp_url

Dear Colleagues,

Department of Pharmacy, Universitas Muhammadiyah Palangkaraya openly inviting researchers with expertise in the field of Molecular Docking to join the new journal that will be released in early 2021, both as an editorial board and as peer-reviewers.

We will call this journal "Journal of Molecular Docking" or "J. Mol. Docking", with a very specific aim and scope, namely various research in the field of science and health using Molecular Docking as its main method.

Currently we are still preparing the journaling platform with OJS 3.1.1.2 and will start collecting articles as soon as the editorial board and peer-reviewer members are gathered.

It should be noted that this position is voluntary, so all editors and reviewers will not receive any rewards in the form of funds. However, we will provide a certificate of appreciation for each manuscript handled, both as an editor and reviewer.

The target of this new journal is to be indexable by DOAJ after the first year and indexed by Scopus and/or ESCI WoS after the fifth year.

For this reason, we expect the willingness and participation of Molecular Docking researchers to be directly involved in the development of this new journal so that later it can become a publication benchmark for research with the molecular docking method.

Once again, we are grateful for the participation of all researchers and hope for their support to be able to create and grow this new journal.

Best regards,

Mohammad Rizki Fadhil Pratama

Department of Pharmacy

Universitas Muhammadiyah Palangkaraya

http://orcid.org/0000-0002-0727-4392

I have a docking affinity of -23.1kcal/mol is it a good result?