@@primalbioinformatics is the things same for DNA? My compounds are rigid I have done blind docking with DNA. One question main what changes one may observe if with same compound and protein both flexible and rigid docking is tried?
@@SimranSharma-i8iRegarding your second question, proteins are basically flexible in the biological environment, but in order to reduce the computational intensity required for the docking simulations, we keep the protein rigid. Flexible docking mimics the real nature of the protein to some extent but not completely (flexibility is given only for a few amino acids). You can provide complete flexibility for the protein and study the protein-ligand complex interactions through a Molecular Dynamic Simulations study. The binding affinity obtained through the rigid and flexible docking may change sometimes but not always.
@@primalbioinformatics Hi, thanks for replying I am facing one problem how things will change If I am docking with A-DNA. Actually, I randomly chose one DNA 3Qk4 and with that, my compounds were showing docking but now after finalizing all the data I am not finding any report with that DNA and that is A-DNA. But with that it is showing interaction. Can I submit my paper with that .
@@SimranSharma-i8i I need more details to answer you. Can you let me know what is the rationale for choosing this DNA and performing docking? Can you Whatsapp me @ 9600420006? I don't check youtube comments frequently.
Dear sir,during the step select from string, I choose 'ARG24,ARG47',and click add,but when I click choose torsion and currently selected, the whole programme is shutdown.what can I do to solve this problem?
@@primalbioinformatics Everything Sir, really it will be helpful for many people there is no proper practical video in entire youtube. Thanks for your reply
thank you for making this video sir
Sir @primalbioinformatics can you please upload covalent docking tutorial
From where did you get box parameters loke x center y center z center values?
We have to cover the entire binding pocket. No default value. The grid box value will change from protein to protein.
How to identify active site for any protein or DNA.
There are many online servers to predict the protein binding pockets. You may try with sts.bioe.uic.edu/castp/index.html?3trg
@@primalbioinformatics is the things same for DNA?
My compounds are rigid I have done blind docking with DNA.
One question main what changes one may observe if with same compound and protein both flexible and rigid docking is tried?
@@SimranSharma-i8iRegarding your second question, proteins are basically flexible in the biological environment, but in order to reduce the computational intensity required for the docking simulations, we keep the protein rigid. Flexible docking mimics the real nature of the protein to some extent but not completely (flexibility is given only for a few amino acids). You can provide complete flexibility for the protein and study the protein-ligand complex interactions through a Molecular Dynamic Simulations study. The binding affinity obtained through the rigid and flexible docking may change sometimes but not always.
@@primalbioinformatics Hi, thanks for replying I am facing one problem how things will change If I am docking with A-DNA. Actually, I randomly chose one DNA 3Qk4 and with that, my compounds were showing docking but now after finalizing all the data I am not finding any report with that DNA and that is A-DNA. But with that it is showing interaction. Can I submit my paper with that .
@@SimranSharma-i8i I need more details to answer you. Can you let me know what is the rationale for choosing this DNA and performing docking? Can you Whatsapp me @ 9600420006? I don't check youtube comments frequently.
Dear sir,during the step select from string, I choose 'ARG24,ARG47',and click add,but when I click choose torsion and currently selected, the whole programme is shutdown.what can I do to solve this problem?
Do you still have this problem?
@@primalbioinformatics
I have this problem know
What should I do??
@@ES-yd1zeWhich version of AutoDock Tools do you use?
@@primalbioinformatics yes!The Autodocktools version I used is 1.5.7,Dec_19_18
I have the same problem. As soon as I choose "residue," the whole programme is shutdown
Sir please upload qsar analysis 🙏
You need 2D or 3D QSAR analysis?
@@primalbioinformatics Everything Sir, really it will be helpful for many people there is no proper practical video in entire youtube.
Thanks for your reply
@@sanjaisrao484 Ok. I will upload it next week.
@@primalbioinformatics Thanks sir🥺
can u share the commands that are shown on right side
DO you still need it?
@@primalbioinformatics yes
I am making another flexible docking video. I will upload it in a day or two. In which i will give those commands in the description.
Respected sir, make a video on docking result visualization like 3D image and 2 D image
I am uploading next week.
Dear Sir ...the whole system is shutting down after select from the string
Try to install lower version of ADT