Very useful introduction to MVD. I started to do docking of some molecules but I couldn't go to the training classes about the use of this program. Actually, it doesn't appear to be so difficult to use as seen from your video. Thanks a lot!
Francisco Can if you like my video share among your friends subscribe to my channel and you want my help in docking in any other software’s feel free to contact me 8919754133 on Watsapp dushyanthreddy233@gmail.com
Your efforts are really very impactful and appreciated, but I have a question please let me know how to identify which cocrystal ligand is active and has to be removed during process...
Subscribe to my lectures and share among your friends I will explain you in detail in other lectures of active ligand identification ....you can contact me on Watsapp 8919754133 I would be highly thank full if you subscribe and share my lectures
Suppose, 1: if I have >1000 ligands are docked with a single target protein and multiple ligands are bound on a pocket/druggability site of the target. 2: Or, if there are multiple sites, say 3 pockets in the target which are bound by multiple ligands. In these cases, what are the criteria/parameters I should follow to choose the best ligand and pocket of the target protein?
Firstly welcome to my channel please subscribe and share my lectures and feel free to contact me on Watsapp 8919754133 country code 91 ....regarding your question you can dock even 10 thousand even lakhs they will bind only to the active site ...secondly in a protein normally has single co Crystal in its active site along with that there may be co factors.....you should select the ligand properly avoiding cofactors ...your query sounds good and logical keep in touch with my channel more lectures and videos to turn up ...have a nice day
You can use multiple ligands at a time and when you are viewing results you should select individually one by one however the best fit ligands are already ordered accordingly
I learned this at class. But i forgot how to allign the ligand to a cavity. Cause when i insert the ligand it just so far away. Could you please tell mr how? 🙏
Purchase the license from vendor .....if you like share my videos subscribe to my channel and feel free to call me on WhatsApp or email 8919754133 dushyanthreddy233@gmail.com
If you have .edu email you can ask for trial version for 30days they reply to email within 4 days . When you obtain the trial license download free software call "RunAsDate" and freeze the date within the trial period so the trial version last for ever . If you face any problem let me know
Please subscribe and share my lectures with your friends and others feel free to call me on WhatsApp or email at 8919754133 dushyanthreddy233@gmail.com
Side chain refinement problem to resolve that you need to prepare protein please subscribe and share my lectures feel free to contact me on Watsapp +91-8919754133 dushyanthreddy233@gmail.com
Depends on the analysis and mostly moldock score please subscribe to my channel and feel free to call me on WhatsApp and send me email dushyanthreddy233@gmail.com 8919754133
First thing is you should know difference between co-factor and inhibitor/promotor in general co factors are used to crystallize protein or they already crystallize along with protein sometimes metal co-factors present in the protein such as 1ZXM protein where you should consider co-factor also as part of active site or else you should select promoter/inhibitor ligand in the protein excluding the cofactors Please subscribe and share my lectures feel free to contact me on whatsapp 8919754133 dushyanthreddy233@gmail.com
And sir on active site selection in Mvd 5 sites are selected then how to select the best site among them for docking or we have to just go for user defined
What you are saying if the protein is already ligand bound you should go with that site ignoring other sites you should check my other lectures tooo for your doubts
@@Dockingbydushyanthreddy no sir I am saying that when we go for docking study we go for detection of cavities now there are 5 cavities which software detects. Now out of these 5 sites which is to be selected during docking wizard
No it’s paid version however you can have a trail version of 30 days ...please subscribe to my channel and share my lectures with your friends and others feel free to call me on WhatsApp or email at 8919754133 dushyanthreddy233@gmail.com
Esti Mulatsari welcome to my channel please subscribe to my lectures and share among your friends and need full.....regarding rmsd it is by defalut displayed in the output file for that please also install molegro molecular viewer and open your output u can easily see rmsd
molexus.io/contact/ try this u need to request for a licence which is available for trial, I cant share u the Product ....u request them in writing they will provide you pls send ur details of your organisation or institute If u like my videos pls subscribe share among your friends
Jaydip Bhaliya molexus.io/contact/ Request them for trail license they will provide you for 30 days later on you need to purchase it ..:: it’s a good software. While requesting license please mention your institute name and affiliation
@@Dockingbydushyanthreddy thank you very much, sir, through your tutorial we have published our research article in a very reputed journal. here its DOI: doi.org/10.1515/jbcpp-2020-0262 now I want one tutorial on, how to draw steric interaction with ligand in 2d format with bond connection illustration.
Great work keep doing please subscribe and share my lectures with your friends and others who are in needy feel free to call me on WhatsApp or email @ 8919754133 dushyanthreddy233@gmail.com
Sir your video is really helpful for perform to docking......but mol dock score result is gave always negative results say my guide. Or my result is positive value of mol dock score.......
