The zero-charge error usually means some atoms are missing charges. Try these steps: Check the PDB file for proper atom definitions. Add Hydrogens using tools like AutoDockTools. Assign Charges manually in AutoDockTools. Give these a try and see if it resolves the issue!

The reference creation part involves collecting relevant academic papers and then organizing them based on citation counts, co-authorships, or keywords. If you didn’t catch that part, you might want to check the section where I explained how to extract data from Scopus or Web of Science. If you still need help, let me know!"

To identify ligands in predicted structures, you can look for the small molecule or compound that interacts with the protein or receptor in the docking results. In AutoDock Vina, the ligand is typically the smaller, non-protein structure within the binding site of the larger protein structure. You can visualize this using molecular visualization tools like PyMOL or Chimera, which will allow you to clearly see how and where the ligand is binding to the target protein.

Thanks for your question! If you're not analyzing data based on affiliation or corresponding author, there's no need to fill in the missing details. Otherwise, it's best to do so. For other types of analysis, VOSviewer shouldn't create any issues.

@@Axonist can you tell me which all analysis are done using corresponding author data in Vosviewer? Can i do the following tests without complete corresponding author data: Co-authorship (Unit of analysis: authors); Citation (Unit of analysis: authors); Bibliographic coupling (Unit of analysis: authors); Co-citation (Unit of analysis: cited authors)?

@@uncletom11000 You can perform the analyses you mentioned in VOSviewer even with incomplete corresponding author data, but there are trade-offs: Co-authorship: Possible missing connections, leading to underrepresentation of collaborations. Citation: You might miss some citations, so results could be less comprehensive. Bibliographic coupling: Reduced strength of connections due to missing shared references. Co-citation: Generally more resilient, but complete data is always better for accuracy. In short, while possible, incomplete data may impact the reliability of your results.

Thanks for your kind words

Thanks for your kind suggestion

Yes, you can manually add the three articles to the CSV file for your bibliometric analysis. Make sure to fill in key columns like Title, Authors, Publication Year, Journal Name, and DOI. If available, include Abstract and any other relevant columns. Once added, you can proceed with your analysis as usual.

@@Axonist Thank you

@@uncletom11000 Your are most welcome dear

Try reinstalling AutoDock Tools or check if the installation is complete; ensure you're following the tutorial steps correctly, as configuration files should generate automatically.

Try it with function key

VOSviewer ka istemal karke bibliometric analysis aur data visualization ke liye document banaya jaata hai.

We're removing ligands from crystallographic files to prepare the protein for docking with new ligands. While AlphaFold structures are useful, crystallographic data typically offers higher resolution and experimentally validated conformations, making it preferable for docking studies.

@@Axonist Makes sense but had a couple other questions: In theory, if the Alphafold predicted structure were to highly accurate (let's say it's at least as good as crystallographic data or better now or in the future) wouldn't removing the ligands alter the conformation of the protein in contrast to it's non-bonded state? How significant is this alteration? Also, would really appreciate it if you could point me in the right direction in order to learn a structured approach to using these tools through COLAB. Is this a viable route? Any disadvantages as opposed to just owning the necessary hardware? How do I master CHARMM? I've been banging my head against the wall for the better part of a year and would be really grateful for any guidance you could provide in this regard.

@@AlwaleedHadaidi Thanks for the questions! Ligand Removal Impact: Yes, removing ligands can alter a protein’s conformation since ligands often stabilize specific structures. Alphafold typically predicts unbound states, so this shift can be significant. Using COLAB: COLAB is a great starting point for learning these tools without expensive hardware, though it has computational limits. For larger projects, owning hardware might be better. Learning CHARMM: Start with official tutorials, documentation, and community forums. Persistence is key-every bit of progress counts! Feel free to reach out if you need more help!

@@AlwaleedHadaidi Great questions! Protein Conformation: Removing ligands can indeed alter the protein’s conformation, sometimes significantly, depending on the protein and ligand involved. This is why some studies start with the ligand-bound structure. Using Colab: Colab is a viable option for molecular docking, especially if you lack high-end hardware. It’s a great learning platform but has limitations like session timeouts and restricted memory. Learning CHARMM: Start with the official CHARMM tutorials and practice running simulations. Gradually, dive into research papers and forums to deepen your understanding. Stay persistent-it’s a challenging field, but you’ll improve with time. Good luck!

No, a 32-bit version of AutoDock Vina might not work properly on a 64-bit system. It's recommended to download the 64-bit version for compatibility.

You can try downloading MGLTools from an alternative mirror site or use a different browser. If that doesn't work, consider checking the AutoDock Vina tutorial for additional guidance or solutions.

Please let me know what kind of issue are you facing....

So nice of you

Please let me know what kind of issue are you facing for autodock vina installation???

No installation issue.. But when I upload a target for docking structure is not visible on the screen

@@iqrahasan9114 If your target structure isn't visible after uploading for docking, try these steps: Ensure the file is in a supported format (e.g., PDB, MOL2), zoom out or adjust view settings, open the file in another tool to check for corruption, ensure correct settings for visualization, use the latest version of the software, and check if Python is installed, as it's required by some docking software. If the issue persists, provide more details about the software and any error messages. Hope this helps!

@@Axonist can you tell me the.. How all binding sites show by using biovia discovery studio??

@@iqrahasan9114I have already explained this in the following video. Please check it out: kzbin.info/www/bejne/pnPIkouFo7uYfa8si=IxPW0rA9pgGmqd9M

First, you should sort your title column with expend selection then you will get non-English titles at the top or bottom of the column. Let me know if you will get any issue.

@@Axonist sir.. I have sorted as u mentioned in the video.. But I m getting some to the titles in other language as well..

@@Axonist also could u plz guide me how can I know the top most publications and the top most articles.

@@poornimav5555 To find the top publications and top articles using Dimensions.ai, search for your keywords or topics and apply filters like publication year or research categories. Then, sort the results by citation count or Altmetric score to identify the top articles. Use the analytics tools for visualization and analysis, and export the data if needed. Hope this helps!

@@poornimav5555 If you're getting titles in other languages, you can manually search for the English titles or use AI support like ChatGPT to help assess and translate the titles of articles in other languages. This can help you better understand and sort your results. Hope this helps!

Make sure you are using latest version of biblioshiny. If problem still persist, just check which one file format is working in biblioshiny like lens.org, diminssions.ai or any other file format. Then convert your Scopus file data to such file format that is working with biblioshiny. If still you are facing issue than share me your file I will try to resolve the issue.

@@Axonist how to share the file sir please tell as I have tried everything already even I deleted 26th row in excel after that it is coming Error- Input string 25 is invalid and it is happening again and again, please give your mail or no. So that I can send you the file 🙏🙏

@@shivamjohar8697 please share me it on [email protected]

@@shivamjohar8697 please share me on [email protected]

@@shivamjohar8697 Please share me your files on [email protected]

So nice of you

Good luck...If you will get any issue, I will be here to assist you as much as I can.

You are welcome!

You can use AND/OR condition to build your query to extract data. You should consider this You tube video for it. kzbin.info/www/bejne/r6GofXh8qNiDbcUsi=p-okft18pRxuf9Xq

Hi @javeriyaAyub, glad you found the video helpful! After identifying the ligands for your protein, the next step involves using AutoDock Vina to perform molecular docking. This process helps determine how well the ligands bind to your protein of interest. You'll need to prepare your ligands and protein structures, set up the docking parameters (like grid box size, exhaustiveness), and then run AutoDock Vina to calculate the binding affinities. Feel free to ask more specific questions if you need further assistance!

Hi @Zack6ix, thanks for the feedback! Glad you liked the visualization. You're right, the types of bonds and their distances are important. Hydrogen bonds, ionic bonds, and hydrophobic interactions each play a different role, with hydrogen bonds often being the most significant. Shorter distances usually mean stronger interactions. I'll consider adding more details on this in future videos. Feel free to ask if you have more questions!

So nice of you. Thanks for your kind words

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

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

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

Thanks brother

You are most welcome 🤗🤗

Please download UCSF Chimera X latest version.

Ensure the "config.txt" file path is correct, the file exists, and you have read permissions. Here’s an example "config.txt" file for AutoDock Vina: receptor = receptor.pdbqt ligand = ligand.pdbqt out = output.pdbqt log = log.txt center_x = 0 center_y = 0 center_z = 0 size_x = 20 size_y = 20 size_z = 20 exhaustiveness = 8 num_modes = 9 energy_range = 3 Double-check your file name and path, and try again.

@@Axonist file name and path are correct I don't know where I'm doing wrong, I have a research project for my bachelors in chemistry and I really want this to work and I need help

@@shahzaib8922 If possible please share your files on my email, I will try to find out the issues.

@@Axonist sure what's the email

@@shahzaib8922 Checkout channel's about us page

If you will login it then you can able to download dataset of 50000 records from it.

Fpocket and AutoDock are great for identifying binding pockets and docking ligands, but they aren't typically used for de novo drug design. For that, consider tools like Schrödinger’s Glide, MOE, or LigBuilder. However, you can still use Fpocket and AutoDock to identify and validate potential binding sites for your new compounds.

Please let me know your source of data. Because if you are using data from dimensions.ai then you can perform analysis for country and organisations

Noted...You will get a new video on the topic soon.

Noted...You will get a new video on the topic soon.

Memory leaks when repairing missing atoms can be tricky. Here are some quick tips: Ensure AutoDock Vina and all dependencies are up to date. Verify they are correctly prepared. Break down the process to isolate the issue. Use tools to track memory usage. Hope this helps! Feel free to share more details if you need further assistance.

@@Axonist thanks for the quick answer, hopefully i can find what caused the problem

Please share your protein ID or PDB file of your receptor protein, and I'll try to resolve the issue.

Please let me know how can I assist you

Thanks for your kind words

Hi! If you're having trouble installing Bibliometrix Biblioshiny, try these steps: Ensure you have the latest R and RStudio versions. Install the package with: install.packages("bibliometrix") Launch Biblioshiny with: biblioshiny() If issues persist, please share more details about the errors. I'll help you out!

Hi! Yes, ChimeraX supports ligand interactions on Windows too. You can utilize the "contacts" and "hbonds" commands to visualize these interactions. Check out the ChimeraX documentation for detailed instructions. If you need a tutorial specific to Windows, feel free to let me know!

Hi! Your concern about ligand charges is valid. To ensure correct charges on ligands when using UCSF Chimera and docking with PyRx, you can: Use Chimera to add charges via the "AddH" and "AddCharge" tools. Verify and, if necessary, manually adjust the charges in Chimera before exporting the ligand for docking in PyRx. This should help maintain the accuracy of your docking results. If you need further assistance, feel free to ask!

Never mind, I found out that ChimeraX allows one to save a file as a PDB.

Hi @professorswenson3504! Glad to hear you found that ChimeraX allows saving files as PDB. If you need any further assistance with molecular docking using PyRx and ChimeraX or have more questions about exploring protein interactions, feel free to ask!

Meng, E. C., Goddard, T. D., Pettersen, E. F., Couch, G. S., Pearson, Z. J., Morris, J. H., & Ferrin, T. E. (2023). UCSF ChimeraX: Tools for structure building and analysis. Protein Science, 32(11), e4792. Kondapuram, S. K., Sarvagalla, S., & Coumar, M. S. (2021). Docking-based virtual screening using PyRx Tool: autophagy target Vps34 as a case study. In Molecular Docking for Computer-Aided Drug Design (pp. 463-477). Academic Press.

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!

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.

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!

Hi! The "could not open config.txt for reading" error means the file is missing or in the wrong place. Try these steps: Ensure config.txt is in the correct directory. Verify the file is named exactly "config.txt". Use the full path to the file in your command: vina --config C:\path\to\your\config.txt Check you have read permissions for the file. Let me know if you need more help!

Hi! To adjust the grid box in AutoDock Vina without using the control button, you can manually set the grid box dimensions in the configuration file. Specify the center and size of the grid box like this: center_x = <value> center_y = <value> center_z = <value> size_x = <value> size_y = <value> size_z = <value> Replace <value> with the appropriate coordinates and dimensions. This method allows precise control over the grid box settings. Let me know if you need further assistance!