Molecular docking for Beginners | Autodock Full Tutorial

Molecular docking for Beginners | Autodock Full Tutorial | Bioinformatics

Рет қаралды 293,756

4 жыл бұрын

The molecular docking approach can be used to investigate interaction between a small molecule and a protein at the atomic level, which allow us to understand the behavior of small molecules in the binding site of target proteins, and biochemical mechanism in b’n protein and ligand molecule.
This video will provide you full step by step manual on Protein-ligand docking using Autodock
MGL Tools: mgltools.scripps.edu/downloads
Autogrid4 and Autdock4 : autodock.scripps.edu/downloads...
Open Babel GUI: github.com/openbabel/openbabe...
Literature:
www.ncbi.nlm.nih.gov/pmc/arti...
autodock.scripps.edu/faqs-help...
www.sciencedirect.com/topics/...

Пікірлер: 298

@ChemWonders 2 жыл бұрын

This video will stand as a landmark in my future studies on docking. Well done and Thank you.

@alannah3245 2 жыл бұрын

Amazingly clear tutorial! Finally got autodock working!! Thank you so much!

@mollylu3638 2 жыл бұрын

THIS IS SO HELPFUL! So clear! I have seen other ones which the youtuber makes mistakes and go back and forth, but with this one I really had the peace of mind and it worked in one try! Thanks so much for taking the time to make this! Already subscribed and will be going through other tutorials!

@kbaitsi 2 жыл бұрын

Really good tutorial, not just what to do but also why. Thanks!

@abdulmalikaliyu8876 4 жыл бұрын

I went through your presentation sir and I was able to understand it. Thank you very much. We plead for more like this.

@jaannawaz2007 3 жыл бұрын

Ur welcome

@abhijeetaher4701 3 жыл бұрын

Dear sir, nice presentation i want to do ligand ligand docking to find out hydrogen bonding possibilities in two different ligand to study interaction, how i can do this

@ajaymanaithiya5014 3 жыл бұрын

I have saw various auto dock videos but your videos are so good and also discuss what would we facing issues during docking and you solved these issues during videos. thank you for giving CMD for docking. because i have facing python she'll error. Thank you very much Sir for making these videos. Most of people made the video but doesn't tell about issue but only your videos I saw which have discussed about also issues along with solve the problem. THANKS ❤️

@JaspreetKaur-ry2nb 4 ай бұрын

hi i am facing python shell error please help me in rectifying it

@mariamhussain5142 3 жыл бұрын

Very useful and easy to follow, Thank you

@rajalakshmimanivannan3503 3 жыл бұрын

Thank you so much for tutorial. It was very useful for beginner and even non biology majors also understood clearly.

@jaannawaz2007 3 жыл бұрын

Glad it was helpful!

@tushardhyani3931 3 жыл бұрын

Thank you sir for this, this is really helpful. please keep posting more content like this.

@jaannawaz2007 3 жыл бұрын

Thank you, I will...

@user-gg7gw7yf4w 3 жыл бұрын

It is very very good! Thank you for work!!!

@dashrathkondhare1136 2 жыл бұрын

Many thanks for wonderful presentation.

@bestofluck2225 4 жыл бұрын

Wow!! Thanks a lot sir, I asked for this last time. It's a great to learn from the begining. Now I would like if you make MD simulation that will help me in my studies. Thanks in advance.

@jaannawaz2007 4 жыл бұрын

Thanks For Watching... Soon we will

@vippanchal8 3 жыл бұрын

Good job! I really liked the tutorial. grateful.

@jaannawaz2007 3 жыл бұрын

Glad you enjoyed it!

@shamalidilhara8505 3 жыл бұрын

Thank you so much sir. Its a very helpful video😊

@Eternitypunklove 4 жыл бұрын

THANK you for this!

@jaannawaz2007 4 жыл бұрын

Ur Welcome

@vanshikarajsharma7314 2 жыл бұрын

Wow, really insightful

@neerajm3049 Жыл бұрын

Thank you very much. So helpful video

@divyarana3637 8 ай бұрын

Very clear sir. Thank you

@chemistrywithharooniftikha3073 Жыл бұрын

Really appreciate your efforts. May Allah bless you.

@jingjingilove9500 3 жыл бұрын

A very helpful guide for a beginner like me. Thank you so much sir. I can understand a lot better after watching this video. I would love it if you can make a tutorial on how to do a controlled covalent docking using Autodock 4 as well

@jaannawaz2007 3 жыл бұрын

So nice of you.. sure i will look on it

@apoorvalongtin 3 жыл бұрын

Great information!

@jaannawaz2007 3 жыл бұрын

Thanks for watching!

@tulsivangari2727 5 ай бұрын

Thankyou..it was very helpful

@ogunoluwamayowa4749 4 жыл бұрын

lovely tutorial

@jaannawaz2007 4 жыл бұрын

Thank U

@mariamaarof4646 4 жыл бұрын

Thank you for the video

@jaannawaz2007 4 жыл бұрын

Ur most welcome

@ExploreMalaya 4 жыл бұрын

very informative ty sir

@jaannawaz2007 3 жыл бұрын

Ur welcome...

@ankitajalan4568 2 жыл бұрын

Hello sir, thank you for explaining so nicely. Kindly explain how to determine probable site of binding. I m working with bovine serum albumin and am finding it difficult to identify site I and site II. Please help me. Thank you.

@prabuddhabhattacharya3490 4 жыл бұрын

Hi, thank you for this great tutorial. It is very lucid and informative. Can you kindly make a video on docking of transition metal complexes as ligand and metallozymes as the receptor protein? It will be very helpful.

@jaannawaz2007 4 жыл бұрын

Thanks for Watching... Yes, soon

@SimranArora-hp5rq 9 ай бұрын

???

@jaannawaz2007 9 ай бұрын

@SimranArora-hp5rq @plz send ur query to Dr’s email Address bbabajan@kau.edu.sa

@SimranArora-hp5rq 9 ай бұрын

@raniaadhamira2954 2 жыл бұрын

Hi thank you for good video ! I want to ask, what if we put xyz randomly as long as the ligan in the cube ?

@BIOLINEHK Жыл бұрын

Thanks for video, could you please tell me, in my case why it shows error "receptor.maps.fald"?

@petelok9969 2 жыл бұрын

Hi great tutorial. I have a question. I typically use a config file but it doesn't contain any information about the GA parameters, so I take it I'm using default patameters? Can I put this information into the config file or can I put it in as a flag into the command lìne? Regards Peter

@hanstsahnang4533 3 жыл бұрын

i love your video. this tutorial really helped thanks a lot, dear sir. can you do a tutorial on how to filter ligands during virtual screening campaign and how to validate a virtual screening protocol. thanks

@jaannawaz2007 3 жыл бұрын

u can check this video kzfaq.info/get/bejne/qqx2q7GF29zTen0.html

@nhungdaothi719 11 ай бұрын

Thank you so much for your video. Can I ask some questions: 1. Do I need to optimize the ligand before docking? 2. How to redock with co-crystal?

@DrFoz-dv7hg 3 жыл бұрын

what is the best docking tool for peptide interactions with protein or protein-protein interactions

@lorenchang2638 3 жыл бұрын

Hello, Autodock reported some residues are missing atom. Actually I could see a non-bounded atom near residue. Guess need to add a chemical bond in between. What should to do next?

@cowboycatranch 9 ай бұрын

There is an AlphaFold 3D structure of my protein of interest in UniProt, but I can't find it in RCSB Protein Data Bank. What can I do?

@ashrafwazir5037 3 жыл бұрын

Thank you for uploading such an excellent presentation.. Kindly if possible upload video about metal docking in ligand and how to prepare paramter file for metal. Thanks regards

@jaannawaz2007 3 жыл бұрын

Sure coming soon.. u can check my published articles.. u will find a tool for metal docking

@ashrafwazir5037 3 жыл бұрын

Thank you for your kind response.. most of the bioinformatics and related field students wait for your tutorials.. please if possible kindly provide the link of the metal docking paper.

@diagnoville6856 2 жыл бұрын

Thank you for the video. How do you dock two proteins? Not protein and ligand

@nguyenthaihoa3297 3 ай бұрын

When I read a paper about andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. The andrographolide compound has a free energy of -3.09 Kcal/mol, but it shows great binding when compared to other compounds having more negative free energy values. I think about pressure, temperature, and pH in the body affecting the inhibitory process

@iJoseph903 3 ай бұрын

Indeed, this variable influences the inhibitory process; it is advisable to do molecular dynamics calculations to complete the molecular docking calculations.

@ameracosmetics 2 жыл бұрын

Hi, Brother Thank you for wonderful video. Please make a video, "How to add atoms in autodock parameter file". Because most of the metals are missing in autodock parameter file. For e.g I am facing a problem in preparing receptor file for pdb Id 1E9Z which contains Nickel items. When i add kollman charges, no charge were added to the nickel. Please let me know how to handle with the metals which are not available in parameter file of Autodock

@ni-hamdeen5994 3 жыл бұрын

How did you get the amino acid in the PyMol ? Can you show this?

@sanjaisrao484 3 жыл бұрын

Thanks

@shaziakhan34 2 жыл бұрын

Nice

@Ricocase Жыл бұрын

Cool video! Is fortran, c++, or python used to predict binding affinity and to what degree?

@gutterball10 2 жыл бұрын

I was able to successfully get up to time stamp @24:32. Upon trying to create the log file, something is going wrong. The log file will not generate in my parent folder. Not sure what is going wrong. Edit 1) Thanks for including the autogrid workaround @33:25. Edit 2) autogrid worked normally the second time I tried it through the regular program, I made sure there were no spaces or funny punctuation in any of the file names or folder names.

@GracielleFreitas 3 жыл бұрын

Hi, when i try to remove the heteroatoms my program open a windows with python error. Do you know this error and do you know how to fix it? I have to do this docking because its my homework from college. my ligand stand so far from the protein and i dont know what to do about it :(

@aravindnesaragi3980 3 жыл бұрын

Very much pleased wid ua vid sir...really really helpful....I have a query sir, while selecting autogrid and after launch it is not going to run....can u plz suggest me a solution ...thank u

@parimalakopalle7639 2 жыл бұрын

Hello sir.. You have explained everything very clearly. It was very informative and easy to understand. I just wanted to ask the fourth amino acid which you selected was Lysine (270) and in the excel sheet it was given for Serine. Please clarify.

@obasajuwinner215 2 жыл бұрын

Yes, i saw that as well. I guess it was a mistake, he should have selected Ser272

@kiranvaghela636 3 жыл бұрын

Hello sir, Will it be okay, if i add polar hydrogen and then i perform repair of atoms in protein structure of receptor to prepare receptor for pdbqt format?

@efedogukandincel2959 3 жыл бұрын

How can you validate your docking method in Autodock / Autodock Vina. Normally, we perform docking process with co-cristalized ligand of crystal structure and calculate RMSD value. If it is less than 2A we can accept that our docking method is good. In autodock we get different rmsd values, reference rmsd and cluster rmsd etc. In publications how'll we state the validation of our model?

@aravindnesaragi3980 3 жыл бұрын

Hello sir, Thank u for ur useful information... but i m getting error while repairing proteins, can u plz suggest me what shall i do?

@shahnoushnayeri1240 2 жыл бұрын

Hi. Many thank for your great description. but i couldnt find autogrid4.exe file. could you help me?

@DrFoz-dv7hg 3 жыл бұрын

I wonder if the best conformation is the one with the highest affinity or the one with more hydrogen bonding as explained by others like Dr. RAVIKUMAR CHANDRASEKARAN and it could have a lower affinity. would you explain, please

@RAVISINGH-hd8hf 3 жыл бұрын

sir how can we keep a fixed conformation that is S or R of ligand while in ligand preparation step

@wafaeaubrey838 3 жыл бұрын

Hi, thank you sir for your clear tutorial. I actually want to learn how to docking so I tried to reproduce your example but i found a problem when i input the ligand.pdbqt file in Autodock tools. It send me this message: error parsing the following line in pdb: Atom 1 C LIG 1 22,000 40,000 32,000 0.00 0.00 +0,055 A Even if I followed what you did step by step. I don't know where is the problem, I even tried with others molecules ligand but the same thing occured. Can you please reply to me. Thank you

@amnahafeez5903 4 жыл бұрын

Plz make detailed video on protein Ligand result analysis as soon as possible.. I need this in my final year research project.

@jaannawaz2007 4 жыл бұрын

Thanks For Watching... Soon we will

@emilijaskrodenyte8341 4 ай бұрын

Hello, my input into Open Babel GUI was SDF file of N4-benzoyldeoxycytidine and when I want to convert it into pdbqt file, it says that 0 molecules were converted. Can you help to understand what is wrong? Thank you sir

@thaoha8446 2 жыл бұрын

Dear sir, the fourth amino acid which you selected was Lysine (270) and in the excel sheet it was given for Serine. Please help me with this. Thank you a lot sir.

@iqrasaleh Жыл бұрын

sir, i could not find the autogrid4.exe and autodock4.exe files on internet? even your link is saying page not found? can you guide from where to get these exe files?

@naveennandu4213 Жыл бұрын

Hello sir, how should we get the executive files like autogrid 4. If anyone knows about that please explain

@mungaimuiruri7607 7 ай бұрын

lets say i have one receptor/ and about 20 ligands, i am supposed to do this for each ligand? or one is enough

@eshwarb2489 3 жыл бұрын

Hi, I have a issue. I'm not able to get docking results as it show error like, FATAL ERROR: ERROR: 3778 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". Can u please suggest how to rectify this error ?

@VikashKumar-cu4jj Жыл бұрын

Good evening sir, I didn't found pdbqt format in openbabel GUI app. What should I do. Could you please answer my query it will be very thankful to you

@zohaibfayyaz7290 Жыл бұрын

i just want to know when you clicked on run autogrid and browsed program pathname from where autogrid4 application came from in that folder

@surprisePharma Жыл бұрын

Hello sir I am taking project on drugs design and chemistry but i have a lack knowledge what can i do for this.

@yvonnesoki4825 2 жыл бұрын

If I go to run autodock it starts and shows the little window for just a second and then nothing heppens anymore… No files are created but there is also no error showing up… What can I do?

@mahimasaraf7757 2 жыл бұрын

Thank u sir but wanted to know at 24.36 autogrid4 come from where??

@lifesciencedecoded Ай бұрын

Sir which software is used to predict the anti-cancer compound ?

@ashirashid5950 6 ай бұрын

Hi i made lipid bilayer using charmmvsoftware and now opened its pdb in autodock. I am tryingbto add hydrogen atoms but getting error message from puthon saying the presence of several non bonded atoms. Please guide me how to fix it.?

@nakulbhardwaj3777 Жыл бұрын

Sir, thanks for such an informative video! I just want to ask if our ligand is away form the protein or receptor then what should we do?

@abeerahassan1847 11 ай бұрын

Same question. Does the program automatically place the ligand in the binding pocket once it is loaded?

@DMilannie 3 жыл бұрын

Thank you very much for the tutorial, it was truly helpful! But I keep getting an error: insufficient grid points. /cygdrive/c/AutoDock/autodock4: WARNING: Unrecognized keyword in docking parameter file. /cygdrive/c/AutoDock/autodock4: ERROR: insufficient grid points. /cygdrive/c/AutoDock/autodock4: Aborting... /cygdrive/c/AutoDock/autodock4: Unsuccessful Completion. Could you please tell me how to avoid that? Thank you.

@muhammadashraf1829 2 жыл бұрын

Is there a video for the installation of Ubuntu, Perl and Autogrid ??

@alchemist1979 2 жыл бұрын

Hi When I Run finally autodock and click on launch It says in .dlg file that .C1.map file is missing What should I do

@jayalakshmi5306 3 жыл бұрын

sir if a person gets a large positive value with my protein somewhere around 2856kcal/mol. In autodock vina i received a normal binding energy of -10.1 kcal/mol with the same target and ligand. What could have gone wrong according to you?

@jaannawaz2007 3 жыл бұрын

ur question is not clear to me. if ur talking about protein-protein docking, yes u will get highest docking energy values, b'c there are many residues are involved in interaction for that reason u will get many h-bonds, vdw, ioinic interaction etc., but when it's come to small molecule u will find very minimal interactions.

@manojdhameja4212 2 жыл бұрын

With vina and Autodock, i m getting very different results.

@stan9095 3 жыл бұрын

When pasting into OpenBable GUI, make sure that the input format is selected as sdf - - MDL MOl format. My ligand file would not convert to .pdbqt until I made this change.

@jaannawaz2007 3 жыл бұрын

Open Banel GUI having multiple options ... check input file format correctly

@aishasaddiqa3788 4 жыл бұрын

hi. thank you for this valuable video. I have tried to run docking using your instruction. I have visualization problem in autodock. the line view of protein & ligand is clear but other views (ball & stick, surface, cartoon) are fade and grainy. can you please help me to solve this problem.. Thanks

@jaannawaz2007 4 жыл бұрын

visualization of docking complex.. Autodock is not a good tool, next video we will have docking results analysis... u can follow the same to create high quality publication images... Regarding the error, reinstall MGL tool software.. if still doesn't work... may be system doesn't have graphic card..

@zoilagandara5726 3 жыл бұрын

If you have the ligand X-ray, it's possible to use it for performing the docking???

@gutterball10 2 жыл бұрын

You would need to convert the x-ray data into the pdbqt file for it to work.

@44sowmiyan59 11 ай бұрын

Very hlpful and thankyou sir! Can you please tell where to get the executable files (autogrid4 and autodock4)

@_rodipit 8 ай бұрын

Hi, hope it will help you - i found them occasionally after autodock installation in C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6

@sumitmallick7951 3 жыл бұрын

thanks for this video. I have a question. How i will delete hetero atoms ad prepare protein for final docking?

@jaannawaz2007 3 жыл бұрын

i already shown in video

@shrirakshaa9166 Жыл бұрын

Hi, thank you for this well explained tutorial. I am facing this while ligand preparation- every time I try adding the ligand it shows an error that ligand.pdbqt cannot be read. Also, when checked, open babel shows a message that '0 molecules converted'. Tried numerous things but none worked out. Can I get any help on this?

@knowledgeseeker9757 Жыл бұрын

convert sdf - mdl mol to pdbqt

@deepaknbotany166 3 жыл бұрын

Sir after watching ur tutorial its very easy to perform docking work its simply superb sir but I have some error after step of run auto dock and I have not getting all other files after docking what I can do sir plz suggest me

@harievignesh7252 3 жыл бұрын

Sir, how to take the average value for setting up the gridbox if the pdb co-ordinates come in both positive and negative signs?

@gutterball10 2 жыл бұрын

Think back to basic math. Include the sign when taking the sum. This assumes the Cartesian grid origin is somewhere in the middle of the receptor, as apposed to the entire receptor getting displayed in 1 quadrant or octant of the 3D grid.

@FreeFall73 2 жыл бұрын

Sir do we have to do energy minimization for the ligand and the protein?

@ameracosmetics 2 жыл бұрын

Adding hydrogens and kollman charges is energy minimization

@keyajoshi3965 2 жыл бұрын

Hello. Thank you for the tutorial. I have one doubt, how do you extract the docked ligand??

@xylee2959 2 жыл бұрын

Hi, Keya Joshi. I same question too... Did you able to find any solution to extract the docked ligand/ inhibitor from the complex?

@maharshidixit3183 3 жыл бұрын

Hello, This video really helped me start well. Thank you for that. But I'm facing an error while repairing the missing atoms. I have 994 missing atoms, and it shows "tclerror: no more menus to be allocated" midway while repairing. What should I do? Thank you.

@bibaswanbiswas1583 2 жыл бұрын

me too. have you fixed this>

@tanyaralli3760 2 жыл бұрын

Sir as I am choosing the macromolecule in grid, again and again it is showing list index out of range. Sir please help me how to correct it

@younessmoukhliss5593 3 жыл бұрын

Hi all, thank you very much for your efforts. when the ligand is inserted, it is placed away from the active site. how can this problem be solved? thank you very much.

@jaannawaz2007 3 жыл бұрын

increase the population size, and increase the grid box size..

@NobodyLikeMe2012 3 жыл бұрын

Can you please do a tutorial on Codon Analysis by using CodonW?

@jayalakshmi5306 3 жыл бұрын

sir when i add my ligand molecule its very far away from my target protein and doesnt fit in the grid box. Can I still proceed for docking? Or something can be done on the ligand? Please suggest

@juanpino2146 3 жыл бұрын

I was facing the same issue, but just proceeded to run the docking, and it worked.

@nikeshdewangan5247 7 ай бұрын

Sir, here I am facing one problem, the no.of torsion degree of freedom for my ligand is 36 I set it 32 to make some bond non rotable but when I was running the programs in last it sowing the no.of torsion is high .so sir please suggest me what should I do to overcome this problem?

@Crokai8 3 жыл бұрын

I am trying to add Sn to the software but don't know how to do it, anyone could shed some light on the subject, please?

@sazan447 Жыл бұрын

why did I miss the file it can't be created, I don't know where the mistakes will be glg file is missed what do I have to do?

@marwanbahaj4974 3 ай бұрын

sir when i want to save the GPF then i get error and shows that you must select macromolecule before writing gpf

@saboor_saifi 3 жыл бұрын

sir pls tell that how should i open .dlg and .glg file in word pad??

@muhammadzeeshanahmed2029 2 жыл бұрын

Thank you for sharing very useful information. I am facing a problem when I repair my protein molecule for missing atoms. The program got stuck and do not further process. What should I do about this?

@JaspreetKaur-ry2nb 4 ай бұрын

same issue with me, it is showing python shell, errors, how to resolve please help

@muhammadzeeshanahmed2029 4 ай бұрын

@@JaspreetKaur-ry2nbReinstall the MGL tools and python and use latest setups for both

@mousegamersyt3398 9 ай бұрын

How can I download Autodock tool, Open Babel and VMD in one folder?

@trueps 3 жыл бұрын

sir Apart from ligand and macromolecule you have another autogrid and autodock file. kindly tell me where i can get those files

@phuongoanhpham1897 2 жыл бұрын

Hi! I have the same question like u, so do u know how to have that files? Can u help me? Thanks

@yvonnesoki4825 2 жыл бұрын

Would also like to know that

@rajalakshmimanivannan3503 2 жыл бұрын

I have one doubt sir, I used pyrx for docking when i was docked ligand with molecule (pdb), it was docked with B chain and showing -9.0 kcal/mol. But docked with A chain is -7.7 kcal/mol (B chain deleted ). Can you please suggest which is right?

@gutterball10 2 жыл бұрын

Isn't it usually the lower negative value, or the negative value with the greatest absolute value? ie.. -9 kcal/mol?

@insight_excursion Жыл бұрын

Where did we get the autogrid4

@muhammadashrafhadirosman3845 2 жыл бұрын

do you have toturial in using aptasuite

@nirmalthirunavookarasu9749 3 жыл бұрын

Sir, the best combination for autodock is 50 GA run and 300 population size only or can we increase it further. If we didn't change GA number of evaluation in accordance with number of torssions will it affect our docking?

@gutterball10 2 жыл бұрын

I think there is a tradeoff between increments and compute time. The larger your population sizes and GA increments, the longer it will take to compute. I suspect these values are chosen to offer a balance between accuracy/precision and a reasonable compute time on a standard computer. If you have a more powerful computer you can probably turn these settings up.