Molecular Docking Tutorial with UCSF Chimera and Autodock Vina

Welcome to our beginner-friendly tutorial on Molecular Docking made easy using UCSF Chimera and Autodock Vina. If you're new to molecular docking or computational biology, this step-by-step video will guide you through the process with simplicity and clarity.
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[@rashmimittal1171]

Sir your videos are highly informative...even a beginner can easily learn from it...

[@Axonist]

Thank you for the kind words! We're delighted that you enjoyed the video. Your feedback is valuable to us! 🤗📺

[@bastavdhritiraj1127]

Thank you very much sir....

[@Axonist]

So nice of you

[@shivanisharma7054]

Very informative and easy to understand 🙏

[@Axonist]

Glad to hear that

[@israelekoro8617]

I will appreciate a video on application of DFT for drug design

[@Axonist]

I appreciate your interest! While I don't have a video specifically on DFT for drug design, there are many great resources online that can provide valuable insights. I recommend searching platforms like KZbin or academic databases for tutorials or lectures on this topic.

[@israelekoro8617]

Thanks once again. Please I am new to molecular docking How do I analyze and discuss the results after the docking of the complex?

[@Axonist]

Analyzing and discussing docking results involves examining binding affinities, intermolecular interactions, and structural changes. In UCSF Chimera, you can visualize the docked complex, analyze binding pockets, and study specific interactions. Autodock Vina provides scoring data for evaluating ligand-receptor interactions. Consider factors like binding energy, hydrogen bonding, and hydrophobic interactions to interpret results effectively.

[@israelekoro8617]

thank you very much for this informative video. I want to know how to get the energy value of the final docked protein-ligand complex

[@Axonist]

To obtain the energy value of the final docked protein-ligand complex using UCSF Chimera and AutoDock Vina, you can check the docking score provided by AutoDock Vina. This score represents the estimated binding energy between the protein and ligand. Additionally, Chimera allows you to visualize and analyze the complex, providing insights into the molecular interactions contributing to the binding energy.

[@mugendidickson2747]

the button left click+ control is not working in my case. how can i resolve this please?

[@Axonist]

Try it with function key

[@professorswenson3504]

What if the ligand is only in 2D format? I tried getting Flavin adenine dinucleotide and they only had 2D.

[@Axonist]

Hi! If you only have a 2D format of the ligand, you can convert it to 3D using several tools. For example, you can use: Open Babel: A free tool that can convert 2D structures to 3D. ChemSketch: Another free tool for drawing and converting chemical structures. Online services like PubChem, which often provide 3D coordinates for molecules. Once you have the 3D structure, you can import it into Chimera or ChimeraX for further processing and docking with AutoDock Vina.

[@komalkanyan1677]

Very informative

[@Axonist]

Thanks for your kind words

[@lucasadriano8012]

Could you explain to me, what happens when we delete the residues? Doesn't this change the structure? Couldn't this lead to an inaccurate result?

[@Axonist]

Deleted residues do not create issues, although you must ensure that weather you receptor protein is having any missing residues then you should model protein

[@lucasadriano8012]

@@Axonist ok , tnks

[@mabcreations751]

8:44 I've problem after this. After entering all values when I clicked OK I got "Chimera Error". It says SERVICE 'LOCAL' IS UNAVAILABLE. SEE REPLY LOG FOR MORE DETAILS. Why is this shown? How to solve issue and perform docking?

[@Axonist]

It may be Chimera was not able to call autodock vina.exe file. Please repeat this process from scratch again.

[@mabcreations751]

I did it many times. But stil getting error.

[@Axonist]

@@mabcreations751 Let me know are you using UCSF chimera X or only UCSF chimera

[@nehacharaya5245]

I have downloaded the software chimera and autodock vina and also protein from PDB but after this I just want to know that in which app this protein will open

[@Axonist]

Please open your protein of interest in UCSF Chimera

[@PJ-eu7zu]

Hi, I was not able to find the compound I wanted to dock from PubChem. Are there alternative ways to go about this?

[@Axonist]

You can consider some other databases like chemspider or construct it manually as 2D and convert it into 3D using open babel.

[@phantomcreamer]

Thank you for the video. I'm looking at a protein that has a ligand binding domain but I don't know what ligand it is. At what point can you say confidently that it is the correct ligand? Is it a certain binding energy or score? Thank you anyone in advance!

[@Axonist]

To confidently identify the correct ligand: Binding Energy/Score: Lower (more negative) scores indicate better binding affinity. Biological Relevance: Ensure the ligand is known to interact with similar proteins. Experimental Validation: Validate with experimental data, if possible. Combining these factors helps confirm the correct ligand. Feel free to ask for more details if needed!

[@jayaupreti1835]

Very easy to understand...

[@Axonist]

Thanks for liking

[@user-si3qb5uk2x]

Sir meri presentation hy uscf chemera per tu usper molecular docking kr b dekana lazmi ho ga??

[@Axonist]

Please let me know how can I assist you

[@saidibrahim1572]

I dont have the option of no id when I try to highlight the ligand

[@Axonist]

Ensure the ligand is loaded correctly in UCSF Chimera, manually assign an identifier using the "setattr" command if needed, and check for compatibility issues with the latest versions of UCSF Chimera and AutoDock Vina.

[@phantomcreamer]

What if you have chimerax?

[@Axonist]

Hi! If you have ChimeraX, you can still perform molecular docking. ChimeraX has powerful tools for preparing structures and visualizing docking results. However, for docking, you'll need to use a docking tool like AutoDock Vina. You can prepare your structures in ChimeraX and then use AutoDock Vina for the docking process. If you need a tutorial specific to ChimeraX and Vina, let me know!

[@Dayogbuji]

Hi, I have tried repeatedly to install the UCSF Chimera software. Your help in resolving this will be highly appreciated.

[@Axonist]

Please install python first and then install UCSF Chimera x

[@HimaMakala]

Very nice video .. Thanks.. Could you please tell me how you export the docked complex as pdb ( if I want to visualize it in PyMol)... thanks

[@Axonist]

Thanks for your kind words. We are working on several videos including network pharmacology, Molecular dynamics simulations, binding free energy MMPBSA or MMGBSA, Gene enrichment analysis and many more. I hope that these videos will be published soon on Axonist KZbin channel. Please keep watching.

[@ajaykumarsharma9020]

Very informative video sir.....I just want to know some other things how can I contact you???

[@user-kp4wo8st8o]

i have performed this. but some errors are occurring. first thing in my protein there is no nonstandard amino acids so i did not do deleting action. once did dock prep it is showing that correct charges are unknown for 19 std atoms names in otherwise standard residues. second error whenever i am adding ligand it is not getting separated from protein. please help me

[@Axonist]

I didn't fully understand your message. Kindly send me an email with details about your receptor, ligand, or complex, and provide a description of your requirements. Once received, I'll be able to assist you accordingly.

[@loafjan2063]

Is it ok if the ligand and protein is covered by the grid box?

[@Axonist]

Thanks

[@alien2883]

Hello sir. Could you please give me the journal link of this procedure. Because i need to cite this method in my methodology section. Thank you

[@Axonist]

Although you can consider any reference from google scholar using search keywork "molecular docking" AND "UCSF Chimera". You can consider following reference also: Butt, S. S., Badshah, Y., Shabbir, M., & Rafiq, M. (2020). Molecular docking using chimera and autodock vina software for nonbioinformaticians. JMIR Bioinformatics and Biotechnology, 1(1), e14232.

[@tanmoychatterjee7922]

Sir please help why the grid box always disappears. A dialogue box appears which shows that the server is not available. What to do??

[@Axonist]

It's possible that there could be a graphics card issue or another technical issue causing the problem. Could you please share the ligand and receptor with me? I'll do my best to assist you further.

[@tanmoychatterjee7922]

@@Axonist how sir? Can you share email id? Actually when I try with me setup it was fine. But in windows 11 setup there was a problem

[@Axonist]

@@tanmoychatterjee7922 [e-mail]

[@user-lp5xh8wv9v]

Sir,am currently a bpharmacy student,for last year elective subject am planing to do a research work on CAAD. is it possible to do anything with autodock..pls relpyy thanku

[@Axonist]

Hi Suvin, I hope you are doing well. Yes, of course you can consider CADD for your research work. Autodock and autodock vina are very powerful tool for molecular docking and virtual screening or high throughput screening work. Although MD Simulations and binding free energy analysis is highly recommended in computational drug discovery. If you have any questions please feel free to contact me anytime. Thank you

[@hanzomain8302]

Can you use the method also to analyse protein protein interactions like antibody antigen?

[@Axonist]

Certainly! While molecular docking tutorials like the one using UCSF Chimera and Autodock Vina can aid in analyzing protein-protein interactions such as antibody-antigen binding, it's important to acknowledge the method's limitations. Interpretation should be cautious, and experimental validation is essential for robust conclusions.

[@darshitasharma4594]

👍🏻👍🏻

[@dr.anuragdabas]

Thanks 🙏🙏

[@Axonist]

Thanks a lot

[@SolomonMakanjuola]

Please how can I reach you I need guide on my dissertation

[@Axonist]

Hi... Please connect me on email [e-mail] Thanks and regards

[@mandeepsarvang9158]

Bruh how to solve problem of win32 application

[@Axonist]

I am not getting you. Please let me explain your issues in detail.

[@mandeepsarvang9158]

@@Axonist sir i mean in opening pdb ot shows that this pdb is not valid for win32 application

[@Axonist]

@@mandeepsarvang9158 It may be happened due to having 32 bit operating system. You might be fresh install of 64 bit windows Os.

[@dadasaheb12377]

Its free software

[@Axonist]

These softwares are free to use

[@dadasaheb12377]

Sir you not covered the chimera installation process ?? 😮😮 Where installed Mean both auto dock and Chimera install in same files or seperate

[@Axonist]

Chimera and AutoDock are separate software programs, and they are typically installed in different directories. AutoDock is a molecular modeling tool used for docking simulations, while Chimera is a molecular visualization and analysis software. Each program has its own installation process and directory structure. When installing these tools, it is recommended to follow the specific installation instructions provided by the developers for each software. Typically, during the installation process, you will be prompted to choose a directory or path where the software will be installed. Make sure to install AutoDock and Chimera in their respective directories to avoid any potential conflicts.@@dadasaheb12377