My own bias is that it is better to start any scientific investigation with a research question or hypothesis. Then think of the things you would need to do to answer the question or test the hypothesis (i.e., the specific aims of your project). The last thing is to determine the methods needed to carry out your aims. You might discover that you do not need docking or molecular dynamics; some other technique might be more appropriate for the question you are asking.

However, let's suppose you are interested in drug discovery, and you have decided that you prefer a structure-based virtual screening approach over a ligand-based virtual screening approach for finding candidate compounds that interact favorably with your receptor. In this scenario, it would make sense to start with ligand-receptor docking. Then molecular dynamics might be used as a follow-up to study the top-scoring ligands and their receptor interactions in more detail. Docking lends itself to high-throughput procedures and is computationally far less demanding than atomistic molecular dynamics.

Docking is easier, try it first then learn molecular dynamics.

Although learning Docking is easier than Molecular dynamics, but note that Docking protocols assign many approximations, therefore, the reliability of the resulting complexes is uncertain, and analyzing the results of stochastic search methods in docking can sometimes be unclear. So, you need MD after docking calculation (It depends on what you intend to do) to confirm the poses found by docking. Why? because the static view provided by docking should be verified by using MD.

In my opinion, MD is an effective tool used to model processes, evaluating different parameters of materials in different jobs, used widely in various fields, and has higher accuracy than docking.

Therefore, I suggest learning Molecular dynamics before molecular docking.

My own bias is that it is better to start any scientific investigation with a research question or hypothesis. Then think of the things you would need to do to answer the question or test the hypothesis (i.e., the specific aims of your project). The last thing is to determine the methods needed to carry out your aims. You might discover that you do not need docking or molecular dynamics; some other technique might be more appropriate for the question you are asking.

However, let's suppose you are interested in drug discovery, and you have decided that you prefer a structure-based virtual screening approach over a ligand-based virtual screening approach for finding candidate compounds that interact favorably with your receptor. In this scenario, it would make sense to start with ligand-receptor docking. Then molecular dynamics might be used as a follow-up to study the top-scoring ligands and their receptor interactions in more detail. Docking lends itself to high-throughput procedures and is computationally far less demanding than atomistic molecular dynamics.

I would recommend to go for learning the molecular docking techniques first, as they prepare the foundation for MDS analyses and it will be easier for you learn it once you've been through docking studies.

for do MD simulation you need initial data( conformation, geometry of ligand and ...) that you must have the data or compute them by methods like Docking (you can do it also by MD but MD simulation are time consuming in compare Docking)@ for do good MD simulation you should did good Docking.

both of them will give you the final result

Once you've learned MD you can switch easily to whatever else. Docking is very easy and automatized, and often you might need MD after docking results. So, first study MD, then docking, virtual screening ecc..

I agree with Rudy J Richardson that these methods are just tools that you can use to answer questions. You don't use a hammer (usually) to tighten a bolt; you pick the appropriate tool.

Biomolecules and substrates are flexible and when a substrate binds to a receptor there is invariably an induced fit: both molecules adapt their shapes to accommodate the other. This essential feature is completely ignored by docking, which uses rigid conformations. This strategy permits rapid assessment of many potential inhibitor candidates but at relatively low fidelity. Molecular dynamics provides some insight into this binding site flexibility but comes at the expense of significantly larger computational expense.

I don't think that you can "just learn" either method without dedicated study. Both methods have nuances and require a significant commitment to master. So, before you commit a fair portion of your life to this, you should consider what questions do you want to address?

First, read the source codes and play with them . . . Was it easy reading? Was it fun playing with?

Actually, the molecular dynamics simulations (MDs) enable you to check the the stability and structural constancy of the complex system (protein-ligand complex) through checking several parameters such as, thermodynamic parameters, RMSD, RMSF, radius of gyration as well as hydrogen bonds, it may will help to see water-bridged hydrogen bonds that will not be presented in docking results.

Based on that I suggest to do docking simulation and then MDs

hi Eshak Bahbah ,

Both the methods have their own importance. Molecular docking is used to study the interaction of two biological molecules (Protein and drug or protein-protein intreactions). MD simulation will give you more clear idea in relation to time that with respect to time what will happen with these interacting molecules.

Regards

I would recommend molecular dynamics. It helps to understand the behavior of a biomolecule or biomolecular fragment over time as well as beautifully characterizes intermolecular interactions. Knowledge of molecular dynamics can have interdisciplinary benefits . For eg. https://doi.org/10.1002/adfm.201807332 in this paper molecular dynamic simulations were used for the rational selection of epitopes for molecularly imprinted polymer - based cancer diagnosis .

I would recommend molecular dynamics, then docking, virtual screening etc..

both of them have a significant role in their job.

Firstly, try to get familiar with MD simulation, then docking.

Molecular dynamics calculations reply to series of specific experimental questions or hypothesis, as well as molecular docking. Read, specifically, papers where MD and/or molecular docking are included in methods. Furthermore, there are series of MD calculations (montecarlo, umbrella sampling, tempered etc).

Your question is very naive.

Molecular docking followed by molecular dynamic simulation

For modelling studies, I would recommend starting with docking software. Then, the best docking pose can be subjected to dynamics studies over multiple nanoseconds to get further details about interactions. For docking, I recommend autodock vina. For dynamics, you can check for yasara.org.

Molecular docking and Molecular dynamics.

You may start with molecular docking.

I would recommend you to learn autodock.

The autodock manual provides you step by step instructions on how to proceed.

Here is the link to an interesting nature protocols paper on docking studies. https://www.nature.com/articles/nprot.2016.051

Molecular dynamics simulations can also be performed on the docked complexes. Tutorials from bevan-labs website is a great place to start.

Start with docking and if you obtain good Ki value, you can use this complex as molecular dynamics starting structure.