Hi Agila, there are many, but I most frequently used autodock and autodock vina

@@scienceaddicted3431 thanks, but autodock is used to find the binding between macromolecules + no of small molecules right..?

Thank you too for watching!

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

did u got your msc program?

Glad it was helpful!

Wow, so glad i could help

Hello Ursula! That is amazing, thank you! Also happy that i was able to help in any way. Please email me at Science.addicted at gmail and i'm happy to provide details

Happy to help at Science.addicted at gmail

I would recommend checking out LinkedIn. Search for computational chemistry jobs, or persons with computational chemistry title. Follow all companies that are operating in this field. Eventually they will have jobs posted. Don't miss on bioinformatics. Genetics is a really hot field and companies are looking for candidates with mixed knowledge and experience

@@scienceaddicted3431 thanks for the advice. I would rather want to know the basics. I want to take some crash course about computational chemistry or create hypothesis on my own. But I don’t know where to start as I am in mid 40’s and it was a 12 years back last I touched chem/ physis book. I work in IT make 6 figure. But TBH I am far away from my successful career that Satisfies me end of the day. 😀.

@Zack Well that is an interesting approach. You can always search through udemy for some courses, or khan academy also has some good theoretical courses on KZbin. Once you get the bases, you can check some recent review articles in the domain. For this i recommend google.scholar.com review articles will have the state of the art and the most current issues that can inspire you if you will want to get into any side projects

Hi! I'm afraid that answering your question thoroughly is out of my domain of expertise, but you can certainly give it a try. Computational chemistry is really an easily approachable and very diverse domain, so you can find a nice that suits you.

@@scienceaddicted3431 Hello sir I have completed PG( organic chemistry), please tell me some chemistry related IT courses. I don't have certain information. I have to know about it Hope you help me. Thank you

Thank you! I have used kdenlive video editor and animation to create this.

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

Hi! You can check multiple structures in pdb, to see if there is any with ligand included. There is an Advanced Search option, where you can filter and refine your search. In case you don't know the binding site on a protein, there is a docking technique called blind docking, where you can search and scan for binding sites on the entire surface of a protein.

Thanks for watching and let me know if my answer clarified your confusion!

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.

Thank you for the encouraging comment! Glad the vide was useful

Hello, thanks for watching! indeed, fortran has/had a huge impact in the development of modern computational chemistry, but I have not included it to this topic, because I would not recommend it to someone who is just starting out whit programming. Although, now that I'm thinking about it, maybe I should have mentioned it in the section together with C and C++, but it's an opportunity I missed. Maybe next time :)!

@@scienceaddicted3431 Hello, we have to know that all the basic programs in computational chemistry and computational materials science are written in Fortran and few of them are written in C or C ++, but the linking between these programs is done with scripting languages like python, tcl / tk, perl and Linux Shell scripts like Bash or C Shell. FORTRAN,C and C ++ are compiled languages and they are made to perform calculations, While that scripting languages are too slow to do calculations. So if we plan to do deep computational chemistry, we have to learn FORTRAN, C or C ++, but if we want to do simple calculations or link between different programs, scripting languages are enough. Thank you.

@@haddouabdelghani6911 very informative analysis

That is a great joint! Do you happen to know Computational chemistry projects/tools that were written in Julia? Can you point me to any?

RDkit is a useful tool. It is widely used especially in molecular descriptor prediction and calculation. I do plan to make a tutorial on it in the future. Thanks for watching!

These comments always motivate me. I have been very busy in my day job, but i have some videos planned

Thanks for your nice comment! I will make everything possible to continue

So glad you found value in my video!

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.

Thanks for the nice comment! Glad you found it useful.

Thanks for watching! Glad to hear you found it useful

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

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)

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

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

Thank you! I plan to continue, and do my best to post every other week. The comments keep me motivated. 😉

@@scienceaddicted3431 haha sooo nice of yiu

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

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