Molecular Docking Analysis | Autodock Results Analysis | Protein Ligand Int | Pymol | LigPlot Etc.,

This video give you a brief on Molecular Docking (Autodock) Results Analysis, in this we showed a tutorial how to extract various scores (Binding Free Energies, RMSD, inhibition constant (Ki) ) from Docking log file of Autodock. We also, shown how to generate 2D and 3D images using various web plot form.
Results Analysis Steps
1. Autodock Docking Log File Analysis
2. Save Best Docking Confirmation to PDBQT - In autodock
3. PDBQT to PDB - using Open Babel GUI
4. 2 D and 3D images - PLP, Protein Plus, LigPlot and Pymol
Autodock DLG file score Description:
1. Binding Energies:
bit.ly/397VNDt
2. Inhibition Constant:
bit.ly/32wfHGX
Tools:
1. Open Babael GUI : bit.ly/3eMgXZm
2. PLP web Server : bit.ly/30g07fS
3. Protein Plus Web Server: proteins.plus/
4. LigPlot+ : bit.ly/3fJ3see
5. Pymol pymol.org/2/
Literature :
link.springer.com/article/10....
bit.ly/3h8Uffm

[@prasanthfrancis1263]

Thank you sir, you saved years for us.... I have searched for many journals and videos to understand how to analyse docking. This video and explanation is so clear. I have never found a video other than this which give complete explanation.

[@jaannawaz2007]

Ur welcome..

[@dr.vijayakumara8768]

the same, here too............

[@aiswaryanath9844]

Yea true...

[@abdullahq.o7131]

Really helpful video. Thanks a lot Doctor. This video and the previous one drastically change my status in my master project from knowing nothing in AutoDock to master it. I really appreciate your effort beyond making this video.

[@elhamabdel-badiea4998]

Thanks for this comprehensive explanation for protein ligand interaction, the best video ever I have watched for this topic

[@lianbonnici5626]

I have to write a very positive comment. Dear Dr. BB I highly appreciate for showing these tutorials. It makes our lives (non-bioinformatician experts) much easier as I can finally understand and replicate this for my own PhD project. Keep on making tutorials :).

[@kasonk1692]

GREAT LECTURE!!! THANK YOU SO MUCH!!!

[@adityanarayansahoo5397]

thank you prof for your effort and dediacations towards new learners. also like to encourage you to providing this type of videos and wish your channel grow more and more .

[@wasifullahdawar6962]

Sir g You are the only one who not work for only to get views but to help someone

[@concept1994]

wonderful explanations in very appropriate manner of video

[@tanushreesingh1999]

Thank you so much Sir for your noble service ❤

[@Howling-wolf.]

great sir thank you, the links in the description are more precious

[@sibbalaacademy9328]

its cleared all my doubts in results analysis Thank you so much sir

[@anandsingfattesingpatil5234]

Thank you so much sirji. Very informative. Nice explaination. Simple language.

[@kumargaurav2492]

It’s really informative… thank you

[@norm1124]

Cobgrats to EXACTLY 10'000 subschribers 👍

[@bitajamshidi8103]

Thank you very much sir. That was so helpful.🙏💐

[@hanstsahnang4533]

best video. your channel is definitely my best thanks alot

[@jaannawaz2007]

Ur welcome..

[@hirenmarvaniya7264]

Very informative and helpful

[@user-hw4cp1dt4p]

thank you so much for the video

[@setyantotriwahyudi4322]

Thank You Sir. Great Video.

[@W_T24]

thank you

[@biomedicalscientistmuhammad]

Exellent ❤

[@1p53gen]

very good explanation. Thank you so much.

[@jaannawaz2007]

Glad it was helpful!

[@radhabane7941]

Thank you sooo much sir 🙏

[@samueljoshua7385]

Thank you so much

[@algerien9703]

Top Really, thank you very much

[@Pearl00Paul]

Thank you for sharing! Did you ever figure out how to interrogate PyMol for the number/sequence of the protein residues that a ligand H-Bonds with? Other than manually selecting it via GUI, I have been looking for a way to do so via the command line in order to automate image generation for large data sets.

[@walterbalansa8192]

Cool. I love it.

[@salaheddinehouache1015]

Thank you for the explanation, I got a question plz in the Rmsd table, which RMSD value we should check to know the docking is correct or not ( I noticed that there are 2 RMSD columns, Ref and cluster )

[@onerekici9840]

thank you...

[@Mandeepkaur-vf9hd]

thanku so much sir . this vedio is very helpfull

[@jaannawaz2007]

Ur Welcome..

[@laloburgos3291]

Hello. These programs can analyze the iteractions of results obtained in autodock vina? I think there isn´t a dlg file in vina and the interactions that vina shows are mainly hydrogen bonds but i not sure if they shows van der waals or electrostatic interactions for vina

[@AmjadAli-zz1re]

Well explained please upload video on Silva database and how to use it for phylogentic analysis and tree generation

[@alphaViolinist]

thak you sir

[@tanveerhasan09]

Nice

[@manojsah6509]

Hi, sir , this video is very helpful to understand molecular docking with binding active site. My question is "How to know active binding site of any other protein for good result of molecular docking?????"

[@ThanhVo-yy4zc]

I have 1 Cl atom in the molecule in the pdb file but after saving it as a .pdbqt file it automatically converts to Carbon. I read a document saying that I need to convert the Symbol Cl to c to avoid understanding it as a carbon atom (the autodock is case sensitive) but I still can't do it. Help me

[@atiyeemami3473]

thank you a lot. I have some questions. what is z score and how can i calculate it?

[@srinithisrinivasan8858]

Sir, can we detect vanderwaal forces,covalent bond,ionic bonds in molecular docking? How to find it?

[@shafnaasmy651]

sir wat is the reference range of reference RMSD and inhibition constant

[@thangdang5896]

Sir, you dropped this *insert meme cheems holding a crown

[@egs8545]

I have heard it is better to use APBS plug in rather than vacuum electrostatics can anyone tell me why?

[@meriemfernini4480]

Hello Sir, thank you very much for your tutorials they made my PhD much easier, plz I want to ask about Drug score , tested several ligands with same protein and they gave the same drug score, these ligands are natural ligands of this protein and some are synthetic . can all ligands of same protein give the same Drug score??

[@mvkishore8954]

I have done docking multiple ligands with pyrx. How I can analytse the results with above said online sofwares

[@niveditabhardwaj6733]

The video was informative..sir ,make video on docking analysis via discovery studio

[@jaannawaz2007]

Will try

[@rahatar]

Hi, im trying to download the Autodock Plug for PyMOL but i can´t find it, could you help me with the link to download it please? and thank you for the great videos they have been so helpful

[@ainunmokhtar1936]

Thank you very much Sir for your video. I appreciate much the knowledge you have shared with us. But I have a trivial question, which I hope you dont mind to answer. May I know what is the specification for your computer running all these programs? Because it seem effortless. I wanted to buy a new laptop dedicated for docking study, could you please suggest? Thank you in advance.

[@jaannawaz2007]

www.lenovo.com/sa/en/laptops/legion-laptops/legion-y-series/Lenovo-Legion-Y540-15/p/88GMY501214?gclid=Cj0KCQiA4feBBhC9ARIsABp_nbUY41jLukpa5CjiD55ACu0U3hBLoUYFcKezajn1OJrZkiBQYEidn1caAr4zEALw_wcB&gclsrc=aw.ds

[@edmundmarinelli5294]

This is a very well done tutorial. I really liked the fact that tools for analysius were carefully and well presented. However there is a problem with respect to representation of the ligand structure. I noticed that when the ligand-protein interaction was visualized in PLP the ligand was flattened and there was incorrect connectivity of the ligand atoms. See at 13:22 and forward in the PLP section. The ligand was also incorrectly visualized in Pymol when it was saved as a .PSE file from PLP; the resulting PSE file also showed the ligand with incorrect geometry and connectivity; see 15:29 in the video. Again the ligand is shown completely flattened with incorrect connectivity and also bond length distortion. Note that the ligand was correctly visualized by Protein.Plus - see 16:51 in the video. Here you can see that the ligand has correct connectivity and geometry. Can you explain why the PDB of the protein ligand complex is incorrectly represented - with respect to the ligand shape and connectivity, in PLP and Pymol? Does the problem lie in the conversion of the pdbqt file of the pose to a pdb by Open Babel , or is it a deficit of the PLP and Pymol programs? I've seen this problem, where the ligand is incorrectly visualized in a few pre-print server papers. I'd really appreciate your comments on this issue. Best regards and thanks for two excellent Autodock tutorials.

[@anandsingfattesingpatil5234]

I m also having same problem. In my case I observed that in different software programs ligand was not connected properly. So is it the problem of programs or ligand got fragmented in the process of docking? What exactly is happening?

[@jaannawaz2007]

Sorry didn’t notice your query. I think you have done nice dissection to my tutorial. Yes, PLP and in pymol I used different docking complex, and I used another complex in protein plus tool. After docking, In pymol, I observed a drastic stereochemical changes in the ligand. I went back entire docking method, I found there is some glitch in the autodock while its converting ligand pdb into pdbqt file. I am not able to figure out what’s exactly reasons behind the alteration of ligand molecule. I am assuming while adding charges (pdbqt), some reactive groups in the ligand might have influenced in alteration of ligand atoms. What solution I found is, I opened the docking complex in pdbqt format in pymol, In terminal I wrote command sort (sort command reorders atoms in the structure), and I saved that file as pdb, I used this complex in protein plus. I didn’t show troubleshoot, in the video as this video is for beginner. Anyway, thank u very much for watching my video, I always feel happy, when the experts rise their comments, it will be great help for me to prepare better videos in future.

[@edmundmarinelli5294]

Bioinformatics With BB I found something unusual when I tried to replicate your tutorial. When the VIN ligand is prepared you see the box which describes gasteiger charges and torsions etc. it gives 5 torsions for VIN ligand . When you go through the docking and look at the dlg file that has the poses that file shows 7 torsions, not 5 . Another problem is that it appears to create additional carbons because C30 is listed. It also has an entry for ‘branch’ or somesuch. It seems like autodock4 has a problem but I don’t know where the problem is. When you take all the time to prepare the ligand and you get torsions are 5 and then you perform the docking and the output file shows 7 torsions that is strange. Note that the retrieved pose does not show additional atoms so far as I can tell. There are other problems with auto dock tools 1.57 that maybe we can discuss later. Might it be possible to send you the files for this run?

[@sayleeshendge198]

@@jaannawaz2007 sir can you give the command sort tutorial?

[@walia5555]

Sir how generate topology file of mutant protein in gromacs

[@hirenmarvaniya7264]

Hello sir, How can I convert Autodock vina result output file in pdb format?

[@hashrafi7148]

would you please make a tutorial for ligand optimization and docking of an unknown ligand (with no available pdb file) with a protein?

[@jaannawaz2007]

Ur question is not clear

[@hashrafi7148]

the pdb file of ligand you used in this tutorial was already available. How about a new ligand?! With no available pdb file?!

[@jaannawaz2007]

​@@hashrafi7148 so many tools are available to create unknown ligand. initially u have to know the structure of the drug/lgand. 1. Draw the ligand/drug and convert into simile or sdf or mol2 format. (For ligand drawing u can use chemdraw, hyperchem or ncbi pubchem (pubchem.ncbi.nlm.nih.gov/edit3/index.html)) 2. if ur file is in smile or SDF format.. convert them into pdb using smile converter (cactus.nci.nih.gov/translate/) if u have further questions u can post ur questions in our facebook group. facebook.com/groups/261045198486665

[@cookwithlacy8236]

sir, in the script-based method in autodock vina the log file does not provide this much information, so how to analyze that file?

[@muhammadrehman4129]

Is there any way or software to analyze protein-protein docking results. Kindly guide...?

[@sundasarshad-ns4rp]

Sir Plz upload a video on autodock vina tutorial

[@rafiyasultana1983]

Sir kindly make a video autodock vina installation and also virtual screening

[@jaannawaz2007]

Thank U ... Soon

[@fnpereirajunior]

great information! is there a minimum value of binding energy to consider that there is formation of a protein/ligand complex or not?

[@chuttikutties8215]

Yes

[@fnpereirajunior]

what is the minimum energy value?

[@sangameshwargh5284]

Sir, how to plot the heatmap?

[@lifesciencedecoded]

Sir can we docked two target site for same disease by single ligand? Sir suppose x naam kaa ek ligand h jo A naam ke target site ko inhibit krra ho , phir suppose wahi x naam kaa ligand B naam ke target site ko inhibit krra ho, to sir kya hum ek saath A ligand ko dono target site(A and B) pe ek he saath docking kra skte h..... Multiple target site docking.... Sir plz doubt clear kar dijiye Agar kar sakte hain to kese ? Nahi kar sakte hain to kyu ni kr sakte?

[@harshitashand9964]

Sir when I am uploading my docking.pdb file PLIP it's showing palmitic acid and So4 in small interaction but my protein is different why is this happening can u please tell me

[@ismaildin69]

Very interesting and informative video kindly can anyone of you can help me. Thanks

[@riyavishnoi59]

Sir how to know the how many active site of amino acids interact with ligand

[@jaannawaz2007]

As i mentioned in my previous docking tutorial, if ur describing active site mean, they already have been identified by experimental studies. you just need to check literature and compare with docking results. if u have further clarifications u can post in our facebook group. facebook.com/groups/261045198486665/

[@shilpasharma8381]

Sir, the confirmation of ligand in PLIP is not looking correct. I am also having the same problem. I am not able to understand the reason behind this, weather the problem is in ligand or protein. Or is it just illusion, I just want to know is it correct? can we carry forward this type of structures. Plz suggest

[@nurulhafizan4984]

Thanks for the useful information Sir. However, I have questions regarding protein plus analysis. I already prepare my protein-ligand complex using pymol and saved it in pdb format file. When I load to the protein plus website, it says that there is no ligand. I don't know why is that.

[@jaannawaz2007]

if u have followed the steps correctly.. i am sure u see the ligand in a protein complex

[@shankuparrynjah7144]

@@jaannawaz2007 i have the same problem as the ligand can be view in atodock as a chain but it proteins plus it doesn't show

[@karreddularaja3756]

hi sir i run auto dock based on vedio tutorials i dont now about Cluster RMSD Run 16 B.E-10.31 C-RMSD 0.00 Ref RMSD 50.72 Run 43 B.E. -9.85 C-RMSD 1.50 Ref RMSD 50.18 in this case which best docking confirmation (16 or 43)

[@worldfitnessgoal]

Sir what is docking log in this

[@jalalkrb5281]

Thank you so much. Want ask you if someone could sending me the Docking program.... My regards.

[@mvkishore8954]

LIGPLOT is free database?It is asking institutional mail ID?S

[@hanstsahnang4533]

please sir can you do a tutorial on how to analyze autodock vina results with web servers cited above or other webservers. thanks

[@jaannawaz2007]

Dear Hans, the above autodock results analysis is identical to the VINA, you have to use little logic to understand the VINA results. It's very difficult to provide everything about each and every tools, as a bioinformatician u have to read papers, and tutorial to understand the function of the tools. Whatever the tutorial you are looking in youtube, they will provide you basic information only, u need to gain the knowledge by doing lots of practice on the tools.

[@niveditabhardwaj6733]

Is there any way to analyse result using ligplot without installing the software..??

[@jaannawaz2007]

Yes... u can do it from PDBSUM online tool

[@fozshub4915]

@@jaannawaz2007 what is the link to this tool

[@shikhamudgal9418]

Hi I am Shikha, PhD scholar at AIIMS Rishikesh. My PhD is on nanoparticles, facing problem in docking nanoparticles using autodock vina. Need your help.

[@jaannawaz2007]

Autodock doesn't directly support some atoms, we have to manually add some paratmeters, and they are different for each atoms.. check this link autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html

[@himanshustudy6112]

HINDI🙏

[@jaannawaz2007]

sorry not possible

[@karreddularaja3756]

hi sir i run auto dock based on vedio tutorials i dont now about Cluster RMSD Run 16 B.E-10.31 C-RMSD 0.00 Ref RMSD 50.72 Run 43 B.E. -9.85 C-RMSD 1.50 Ref RMSD 50.18 in this case which best docking confirmation (16 or 43)