Welcome to the Axonist, the pioneering RU-vid channel led by a team of tech aficionados and industry experts. Axonist is committed to delivering high-quality videos that showcase the cutting-edge advancements, breakthrough discoveries, and game-changing ideas that shape our modern world. Axonist is more than just a RU-vid channel; it's a vibrant community of tech enthusiasts who share a common passion for innovation. Thank you for being a part of the Axonist community. Stay curious, stay inspired, and let's explore the future together! #axonist #bioinformatics #python #artificalintelligence #ai #datascience #excel #research #bibliometric #laravel #rlanguage #statastics #analysis #visualization #dataanalysis #videoediting #scienceandtechnology #how #tipsandtricks #advance
@@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!
@@iqrahasan9114I have already explained this in the following video. Please check it out: ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-pBeaXOnVeGM.htmlsi=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.
@@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!
I am unable to import my CSV file of Scopus into biblioshiny as it is showing as Error-Input string 26 is invalid . I am struck from last 2 days mam, please guide me as my research is suffering due to this issue.
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 🙏🙏
You can use AND/OR condition to build your query to extract data. You should consider this You tube video for it. ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-ypELEFssP7c.htmlsi=p-okft18pRxuf9Xq
Hi. great video. I have a question after finding out the ligands of our protein. the next step of ligand best match is confusing i could not get it. Kindly help me out, please
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!
best visualization i've seen so far, could've explained the differences between the types of bonds, which one is more significant and also the significance of the of the distance.
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!
@@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
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.
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.
Sir, while repairing missing atoms of some large proteins, there is an "TclError: no more menus can be allocated" is being shown. Followed by, application crash. Please enlighten me and help me to solve the issue ASAP. (URGENT)
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!
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.
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!
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!
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
@@pytopia5988 Hi! Thanks for your suggestion. Yes, I can definitely consider making tutorials on using Avogadro. Stay tuned for upcoming videos, and feel free to let me know any specific topics you're interested in!
Hi Sir, I faced a problem when installing the software, hoping you can help me out My MGLTools are unable to read the protein i download from PDB and show swig/python detected a memory leak of type 'BHtree *', no destructor found. Please Help
@@AxonistThank you for you reply Sir. However, I'm still unable to read molecule It shows no (0) molecule detected... Is it because I'm using Window 11?
@@jinx3725 The error indicates a memory leak issue in MGLTools. Try these steps: Ensure MGLTools is compatible with Windows 11. Re-download the PDB file. Update MGLTools to the latest version. Verify the PDB file format. If the issue persists, please share the PDB ID, and I'll take a closer look.
Hi! The first data set in the tutorial was obtained from a bibliographic database like Dimensions.ai or Web of Science or Scopus. You can download similar data by searching for relevant research articles and exporting the citation data. Let me know if you need more details on how to do this!
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
