How to start a molecular docking project? | 4 steps for successful molecular docking PART 1

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Molecular docking seems deceivingly simple at first glance, but several computational chemistry factors can influence the quality of the final result. Anyone who is research naive can generate artifacts, unrealistic results without realizing.
Molecular docking tutorials with AutoDock are widespread, however practical steps will need to be taken into account before starting the work.
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12 сен 2024

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Комментарии : 28

@scienceaddicted3431 3 года назад

Let me know if you have any suggestions for next videos. Part 2 of the tips and tricks is in the making.

@scienceaddicted3431 3 года назад

I'm also an avid linux user, so I was thinking to make a series of tutorials for linux usage in bioinformatics/computational chemistry. Linux is essential for automation processes... let me know

@riyaazahamed3007 2 года назад

Sure Mam I’m waiting for that series

@thaleskronenberger8636 3 года назад

I really like this series of videos with the limitations, we are often aware of the chemical properties that they derive from, but not quite a direct application as such.

@scienceaddicted3431 3 года назад

Thanks! Glad to hear you appreciate hearing about the limitations. I saw many tutorials talking about how to do docking from start to finish, but not many will talk about the practical pitfalls and limitations to watch out for. Let me know if you have other ideas to continue the series.

@esmeralda_jenn 3 года назад

It was a perfect video for me, as I am learning molecular docking to use in my thesis! Thank you!

@scienceaddicted3431 3 года назад

You are very welcome! So glad it was useful for you! Good luck with your thesis ;)

@scienceaddicted3431 3 года назад

You also may want to check video part 2, I discuss other practical aspects such as to take into account protein flexibility or to check the data from pdb

@binnuboban9800 2 года назад

U explaination tips provided help for me in studying molecular docking for my research. It made me help to get a perfect plan to go on with. Please update with some more videos. Best brieffffff explanation

@riyaazahamed3007 2 года назад

Nice information about molecular docking….thank you Mam, and pease continue the videos of scope in computational chemistry and molecular docking

@ggezwpgjnpgaming2186 3 года назад

Keep making videos! Thank you!

@scienceaddicted3431 3 года назад

Thanks for visiting the channel :)! Really appreciate the support.

@tbarthakur 3 года назад

Extremely useful tips. Waiting for more such videos. I am learning molecular docking for my PhD thesis

@scienceaddicted3431 3 года назад

Glad to hear that!Good luck with your studies and research!

@ryadrahal9029 9 месяцев назад

thanks it help a lot !

@rajanyasarkar242 2 года назад

Loved this tips and tricks. I am an undergraduate student and I really want to take this up in my Masters or PhD projects! Could you just give me a roadmap for beginners int his field so that I can apply it when I go for research projects

@scienceaddicted3431 2 года назад

I recommend checking out review papers (you can use google scholar searching platform) on the topics you are interested. You can find the most recent/most relevant papers and state of the art on the field

@rathidasgupta Год назад

An excellent overview of the elements of docking. Is it possible to show step by step one such exercise as a template example?

@user-rl5ti6ze4m Год назад

Спасибо. Очень просто и доступно!

@oussamamerzouki2179 2 года назад

Can u please do a full example for docking and thank u so much for these informations in this video keep going 💪🏻

@scienceaddicted3431 2 года назад

That is a good idea. Are you planning to use docking in command line environment or in a user interface?

@matthewadihonneyamos8723 Год назад

Thank u for this educated video. I have a question, do I have to minimize the energy of the ligand that I've downloaded from PubChem ? Thank u

@magedaziz3109 3 года назад

It is very useful content. Keep on. I hope to be professional in ligand docking on the MOE program as a drug discovery scope. If there are any courses in this scope you are present it, please let me know. I hope to connect with you.

@scienceaddicted3431 2 года назад

Hello! Thanks for your comment. I wish you to become the professional on the MOE and many other comp chem programs. It takes time, but anything is possible if you invest time and effort.

@AhmedAli-vq7oy 3 года назад

Thank you very much I hope you will continue your videos until how can we follow the correct way to write a paper. I have a question, If I have a ligand with a positive charge what is the correct step: make a protonation step for my ligand or not?

@scienceaddicted3431 3 года назад

Hi Ali, if you know that the ligand is positively charged, then yes, you should add the corresponding number of hydrogens, according to the protonation state. eg: R-COOH (carboxilic acid - formula with neutral charge) vs R-COO- (carboxylate ion - formula with negative charge)

@AhmedAli-vq7oy 3 года назад

@@scienceaddicted3431 Thank you very much. Kindly I will send an email to you to describe my point.

@scienceaddicted3431 3 года назад

Thanks you! Great to see such interest in correct preparation of ligands