Hi there’s no Ec number of 2HNT on my computer

I also have another question: is it possible to download the spin superimposition movie?

Thank you for your video. I wonder can I use %id to report the similarity between two proteins? For example, for the protein A and protein B comparison, %id is 80. Could I report that these two proteins share 80% identity in structure?

Thanks for this video. I see you have autodock plugin in Pymol. I have been trying to plugin Autodock Vina to Pymol on my Linux system, but can't seems to get it done. Can you please explain or do a video on this. Thanks.

Finally, no Indian accent bioinformatics tutorial . Thanks for sharing i can share this video with Undergraduate students.

can u please explain the seed sequence alignment in this video?

thank you, it is a very helpful video.

Can you tell me exactly where do I download the PDB file? Where's a download button?

When I try to download the ligand summary report , I cant find the excell option, only csv.

Thank you so much for this tutorial. It's so clear and easy to understand. I really need this tutorial to do my research. Once again, thank you so much for the help!

thank you very much!

M facing error while converting my protein to macromolecule( pdb id 4UTC)

Very useful, thank u.

Professor are you sure autock vina is autonomous coordinate x,y, z 25 ? For me it is important for my research I am looking forward to reply

Hello ,i wanted to know while performing vina through pyrx ,the grid is automatically predicted or we have to set it ,as in pyrx the grid is itself set at the centre ...plz help me in this

Is the grid box generated is auto is it necessary to change grid box size.

great video! I wanted to know why the following steps were skipped: removing water, adding hydrogens, merging non-polar hydrogens, and adding partial charges? I'm not familiar with PyRx

Hello, I have doubt that the free version of PyRx software is sufficient for publishing the docking studies.

Hello, I am using the latest PyRx free version software. I follow all the necessary steps required for docking that were mentioned in PyRx tutorial videos. But, here the problem comes when i visualized docking result in PyMol/ DS visualizer as the interacting partners and H-bonded amino acids were different from the interacting amino acid which were already published in peer journals. I repeated same for many protein n ligand exactly same which were given in published papers, but everytime result is same. i pushed n tried very hard but nothing is working, so please help me. You can hands on this- PDB ID-6LU7, ligand- Lopinavior, if the docking with PyRx is fine, then docking result must shows same interaction as in picture or u can see in article. doi.org/10.20944/pr... Thank u in advance

good work

Hii Dear, I am not getting any option to download ligand summary file in excel form.

thx

Please tell me the difference between dali search against pdb 25 vs pdb 50 vs against all? Also how can I remove the redundant results?

what if I want to dock novel derivative which I have designed?

Thank you so much, dear sir, for this awesome tutorial. I am only beginning my PhD and your video helps me getting started.

Thank you, Professor....

Excellent tutorial. Sir, please make a video on molecular simulation of protein ligand interaction using Gromacs

love

much needed ..i liked it very much...

thank you, its very helpful

sir can u please explain the same for Linux users

This is a wonderful tutorial. Thanks a lot.

how did you get promol onto your Mac? I can't open an exe file and the zip file won't download the software.

Very useful thank you

how did you download ProMOL onto a Mac?

Great work.

Awesome tutorial, it worked down to the letter!! I used TextWrangler and Numbers but achieved the same results, thank you sir.

why its says ive downloaded 0 files?

thank you. great tutorial

Best PyRx tutorial I've found yet, thank you!

Thanks!! Very useful!

Thank you for this tutorial. Much appreciated and liked!

Excellent as an idea. Works very nice on Windows, but on Linux this product is a total disaster and that was the main reason I didn't buy their non-free version. First, in 2016 they release ... 32-bit software! Second, the installer is very primitive with having no any idea how to match the library dependencies. There are no deb or rpm packages released for 0.8. Also no any documentation accompanies the installer. And if you have no deep knowledge in tracing code execution you are totally lost at this first step, because you have to install all libraries that the installer needs without knowing their names and versions in advance. Fourth, along with the PyRx code they are used to supply a lib folder containing custom compiled libstdc++ library which in most cases cannot be loaded locally because of a glibc version conflicts. And that particular problem with running PyRx 0.8 you can face on almost all modern Linux distributions (Scientific Linux 7, Ubuntu 16, CentOS 7). The only way one could solve it is to get rid of their libstdc++ libraries and relay on the 32-bits ones brought by the packaging system of the distribution (which ultimately excludes Ubuntu 16 because there is no 32-bit support any more). Note that the same problem with libstdc++ also exists in USCF Chimera. Fifth, because of the direct rendering implemented PyRx is very sensitive to the video driver libraries. Especially if you are equipped with NVidia. You have to have the original NVidia drivers otherwise PyRx mysteriously crashes with no indication what may cause that problem. I hit the same problem with other drivers. I hope these significant problems do not exists in 0.9.

When I type in the command fetch 3oxc, the command window says "it's unable to load '3oxc' ". Do you know what the problem is?

Great video! Could you please tell which PyRx version you used in this tutorial?

Very good video. I have linux(ubuntu), it would have been lot more good if the installation is explained for the same