Autodock Vina Tutorial | Molecular Docking for Drug Design | Lec. 10 Part 2 | Dr. Muhammad Naveed
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- Опубликовано: 21 авг 2024
- Links to download required software:
Autodock Vina
github.com/ccs...
MGL Tools
mgltools.scripp...
Python
www.python.org...
Discovery Studio
discover.3ds.c...
PyMol
pymol.org/2
Site-specific docking using Autodock Vina, Discovery Studio, MGL Tools & Python. Computational drug design and molecular binding site analysis.
In the field of molecular modeling, docking is a method that predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions.
Schematic illustration of docking a small molecule ligand (green) to a protein target (black) producing a stable complex.
Docking of a small molecule (green) into the crystal structure of the beta-2 adrenergic G-protein coupled receptor (PDB: 3SN6)
The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced.
Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site. Characterisation of the binding behaviour plays an important role in rational design of drugs as well as to elucidate fundamental biochemical processes. #AutodockVina #DrugDesign #Docking
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Thanks to your video, I was able to amaze my teacher with a great score on my exams. I can't thank you enough for your help! You're awesome! 🎉👍
Glad I could help!
I watched many videos related to Molecular Docking but your lectures are best
Thanks for such easy and amazing lecture on docking otherwise it to hard to learnt docking by-self or via internet.Also special thanks for technical support for the completion of docking work.Lot of prayers for you by Allah Almighty.
Always welcome dear
@@Prof.Dr.MuhammadNaveed sir kya ap mjy paid base pa docking perform kr k dy skty hain 20 ligands k sath? meri delivery hony wali hai ar mera project ka viva hai 14 date ko ar meri mam kuch bhe baat sun'ny k liye tyar nhe pehly main ny pyrx pa kea tha to unho na mjy compunds change krny ko bol dea us k baad mere pass dobara pyrx bhe nhe chla ar ab mere pass dobara docking ho nhe rhe jis tra require hai k interacting residues wagera show nhe ho rhy hain wo bar br reject kr rhe hain kindly meri help kr deyn
Best explainer...Best teacher..bestest advisor🥰🥰🥰keep it up sir g...Allah ap ko bhtt bhtt kamyabi dy... Ameen sumameeen...
Informative lecture...
Bestest zbrdst Sir g you are doing really excellent 👍
Thanx alot dear. Same for you
Amazing tutorial about docking which I have seen so far. keep it up sir. waiting for more videos also on the analysis of the Molecular Docking
Thank You
welcome and sure dear
@@Prof.Dr.MuhammadNaveed Sir I have sent you an email about the links regarding downloading the software.
I believe more people will benefit from your video(s) if the explanation was in English. Your title is in English you can as well deliver the lecture in English sir.
sure and will start lecturers series in English in near future
Sir I need your help humne I tasser pay protein sequence Dala tou sari detail mil gye wohe 3d structure humne yaha use kare gay aur us main Jo co-factor diya hain wo bhi per co factor kase kare wo ni samjh aarha
i have download MGL TOOL 1.5.7 and there is no grid option there now how am i supposed to save my file in pdb.qt and to carry out work through grid box
Try to reinstall it
After command prompt config conf. txt -- log log.txt here what is log.txt.
By the way i stuck in this point because next stops r not working.
Share your screenshot on email so we may resolve your issue. You can consult my Teaching Assistant Muhammad Aqib @ aqibmirza67@gmail.com
Updated/Accessible Links for the Required Tools
AutoDock Vina
vina.scripps.edu/wp-content/uploads/sites/55/2020/12/autodock_vina_1_1_2_win32.msi
MGL Tools
ccsb.scripps.edu/download/262
Discovery Studio Visualizer
discover.3ds.com/discovery-studio-visualizer-download
PyMol Visualization Systems
pymol.org/installers/PyMOL-2.5.2-Windows-x86_64.exe
Python 3.10.5
www.python.org/ftp/python/3.10.5/python-3.10.5-amd64.exe
Thank you so much, Dr. Naveed
Welcome dear
Sir what will have to do for blind docking...
do docking and compare results of binding affinities
sir ye ap ny ligand ka btaya jo already available ho agr hm khd sy koi new ligand bnana chahty hen jesy kisi phytochemicals sy to uska kya method hoga kindly wo b bta den
then you need to use chemdraw
Very well explained by you..Sir its really helpful.
Please sir its my humble request upload a video about "Density Functional Theory"...please sir..
Stay blessed sir
added to queue
@@Prof.Dr.MuhammadNaveed
JazakaaAllah and bundle of thanks respected sir..😊
Aoa Sir
I have performed docking of the same protein and ligand with
1) Internal MGL tool > Run >
1) Auto Dock
2) Auto Dock Vina
2) Used Command Prompt with command line as you mentioned in the video lecture.
But I got different result for all the three method. All of these showed somewhat difference in the binding energy and RMSD value. Using auto dock vina and similar command line show points difference in Energy values and 0 RMSD for the top rank hit where using the auto dock tool of mgltool gives difference in both energy and rmsd value.
Now I am confuse which one is right and which one is not? Which one use in the research? Or my docking method is wrong?
Please help me in this regard. I will be oblige to you❤️
For our complex such as synthesized transition metal complex how we can create its pdb file? Kindly show an example
Dear Sir, thank you for your nice and informative video. Sir, how can I set grid box parameters so that it fits itself into the middle of the binding site of receptor? And how to know which type of values should be given?
Sir, I also want to know how to perform molecular dynamics for receptor-ligand interaction. Please, make video on that topic.
We will soon make a video on md simulation. You have set the grid box according to binding sites that can be find through COACH OR any other tool
sir agr hm predicted zinc library compounds ko target protein k sat dock karengy autodock vina k through tu osko kaise karengy? wo tu full 3 hazar compounds hai single ligand nhe hota.. plz ye clear krdy mera research hai
for vina you need to select compound first then go for docking and you can get that from any available data set
Thanks sir for giving me authentic knowledge about molecular docking.
Dear sir, i want to doing MS in Biotechnology at UCP with your reference, if u allow me. Otherwise not...
welcome dear
@@Prof.Dr.MuhammadNaveed inshallah August 2022, When admission opens at UCP then I will apply for MS Biotechnology and I will meet u sir inshallah
@@Prof.Dr.MuhammadNaveed Thank you so much, sir, For your valuable lectures. I have an issue with the installation of the autodock vina. No icon of installed autodock vina appears on my desktop or somewhere else after its installation. I have downloaded and installed it many times but could not succeed.
aoa sir..sir ya docking hm na krli h to ya drug designning ma hmri hlp kesy kry gi..i mean k hme pta lg gya k ya ligand h is na yha attach hna h smjh aagai.. lkn aagy wo ab drug ma kesy use hoga?? plz rply
then you must watch my complete lecture series on Computer-aided drug design then you easily understand why docking is important
ruclips.net/video/-fTw-_FzASE/видео.html
Very well explained...
My question is ...if we dont know any thing about ligend and active site thn wht should we do...
ligand is any molecule having ability to bind with central atom to form a complex and the active site is the region where the molecule binds
Then must see my video on I-Tasser as there you can find how we can identify the location or position of the active site. other way Autodock vina automatically identify the active site as the default just not that X, Y Z size for docking ok
Thnk u
Aoa.. AutoDock vina and pyrx both have somehow same working style but which one will be best. And one thing more in pyrx jb hm 2D diagram open krty hain different orientation main tu same 2D diagram ati hai ligand ki conf k lie hr ek ki.? :(
autodock is the best
Good afternoon sir. I have a problem in producing log.txt file in vina. docking was done and then in command prompt, binding energy chart is also shown but log file was not found. How can I solve the problem?
dear log files are downloaded by adding 2nd command mentioned in video then all files will be downloaded in C vina folder and will open in visualiser tool like Pymol
Sir i have questions!
1st: at the end of lecture you typed log.txt file but where to get that file?
In a reply you said that watch my previous video but in the previous video you didn't tell anything about that log.txt file
2nd: even i have saved conf.txt file with proper format in the vina folder but the cmd is showing up that it could not open conf.txt for reading, even my system is uptodate!
Kindly help in this regard!
Its python language which give path to read our grid values
Sir, If a protein's active domain is between 600 to 700 and my comes less than 500, what could be the reason?
then must check other variant of same protein on PDB
Sir ramachandran plot use krny ki or us k results interpret krny ki bhi video banany.
Sir after docking i want to do MD simulation but i am running windows 10 pro and my computer configuration is i5,ram 4gp ,hardisk 1 teri. can i run this into my this configuration.If not so how much feature is needed to do that.
yes possible but run tool according to specs
@@Prof.Dr.MuhammadNaveed "specs"? Sir sorry i am understand this word.
@@fahimalamnobel4789 System specifications
@@Prof.Dr.MuhammadNaveed sir i want to simulate via gromacs which only run on linux.So you mean to say when i run this,i should follow the step by step very carefully ?
@@fahimalamnobel4789 no, their is different procedure for it
thank you so much sir, for your excellent lectures.
pleasures
Sir, I follow your steps, but when I select the grid and choose the macromolecule then error appears "index error", how can I fix it. Plz give tbe solution with steps. Bdw very informative video.
There might be error in PDB structure. Try using another structure
Best/Great work sir.
pleasures
AoA sir thank u.i want to ask that how we dock 2 drugs or 2 molecule with our protein at a time?
Yes it is called multiple ligand docking. We will soon make a video on it.
Sir you are wonderful
Welcome dead
Sir how to dock multiple proteins with a set of 100 ligands? ( 100 ligands with 10 to 20 proteins)
use pyrax
Sir how can we dock a rigid protein with multiple flexible proteins at once?
then use cluspro
Thank you for explaining so well sir but I had issue regarding my discovery studio. Whenever I open the studio it mentions that BIOVIA discovery studio 2020 has stopped working. Can you please guide me what should I do? There’s no storage issue in my laptop .
There might be an issue with the dll files some may be missing or your windows files may be corrupted. Reinstall a fresh version of windows and then try.
Going to perform this tomorrow. Thank you sir
good
Asslam o alikum sir . I do all steps, stuck at the grid step VINA folder is missing.
find in program files and paste conf file there
Thank you, sir it's worked
How to make a protein-ligand complex after vina docking for nma simulation?
last step file can be used for any kind of visualization
My system is not supporting discovery studio of 64 bits ۔۔۔it is supporting 32 bits but i don't have it can anyone please inform me how to download it?or provide a link to download
respected sir!
whenever i save my protein pdb file into pdbqt it gives an error showing that there is no non-bonded atom present.... and hence file is not converting into pdbqt
how to overcome this kindly guide me sir...
then use any alternative protein structure means same protein with different PDB ID
Hello sir if you could make a video related to discovery studio visualization simulation, it would be great for us. Can you please make a video regarding this topic?
sure in queue
Hello Sir I'm currently doing my research work. While giving commands my Docking is not running it gives me this statement
C program is not recognised as an internal or external command , operable program or batch file.
I tried a lot but every time same thing happen. What should I do Now???
Very well explained!!
sir hamy kese pta chlta h k kon sa cofactor use krenge ?
for example I have Niacinamide and now me kon sa cofactor lgaungi?
receptor ligand interaction
amazing lecture. can i ask that i have install all the software but my VINA folder is not seem in drive C please reply.
check in program files
Assalam o alakum i am a research student i am finding difficulty with the installation of autodock vina. i tried for so many times but I cant install it instead of auto dock vian simple autodock install. kindly guide me how I can get through this difficulty
waslam follow link available in description
Well explained
pleasures
Assalamualaikum sir. I get a problem in docking. I want to dock my ligand with an allele (HLA-A*30:02) but I can't find it in PDB and UniProt anywhere. So what should I do now. How can I get this.
then need to draw structure by chemdraw
@@Prof.Dr.MuhammadNaveed But I haven't find the fasta seq also, so how can I draw that
Sir i followed your complete tutorial but i am getting only 2-3 readings in command prompt result, why is this happening sir?
2-3 reading means?
Sir how we can perform docking between multiple Epitope and HLA alleles .
watch my lecture series on CADD
Thanks for the best explanation I've found on the internet, but I have a question, what is the content of the log.txt file?
dear see my first lecture of docking where script written clearly
Sir, How will I identify the active sites of target protein for ligand binding? Is it just assumption to set the Grid box?
Best way to find out by I-Tasser homology modelling then target those residue in grid
@@Prof.Dr.MuhammadNaveed sir how exactly can we target those residues in grid?? i am really confused about active site selection.
@@Prof.Dr.MuhammadNaveed if we don't find active site already than is it possible that the software will automatically select possible active site?? and if so than how accurate could be our results? can we use those results in thesis? or s it compulsory to perform active site prediction step?
Sir it will be good if you provide link to download softwares here in box.
dear already mentioned in the description as well as in part 1
Sir maine saare stepwise perform kiya , but last time main vina(764kb) open hi nahi hora hai , window mera 8.1 hai sir.... Plz help me sir
re install
Sir in my system vina folder is not shown in C drive.. so what i can do ??
check all program file
Dear Sir, Salam, I am facing the "Parse error on line 11543 in file "1FIQ.pdbqt": ATOM syntax incorrect: "Mo" is not a valid AutoDock type" trouble on Autodock vina after giving the job command. Please guide me to resolve that issue.
install vina again
Assalamualaikum
Sir I've followed the video every single step but in command process it is giving some parse line error and some times cannot read config file
Can you please help?
sir I could not find the vina folder in C drive so I could finish the process
Dear ! {C:\Program Files (x86)\The Scripps Research Institute\Vina} ----- try this path
How can we find that this ligand will bind with that protein. kindly solve my querry
on pymol and watch my lecture on it
Sir i faced problem during cmd run... It's shown error - could not open "conf.txt" for reading.
Please help Sir
Repeat it and put all files in C derive
I have a issue in last step kindly reply today
Just follow last step as in video means save log file in C derive
Sir can you please tell how to get the active residues from the docked protein
PyMol
@@Prof.Dr.MuhammadNaveed thank you
sir, which software you have used to convert SDF file to PDB format?
Sir is it possible to conduct docking of nanoparticles (as a drug)?
Dear sir, I went through all the steps successfully, but i couldn't generate the log.txt file, instead i tried with only the conf.txt file and the command prompt only gave 3 results.
Sir, can you sincerely guide me about how to generate the log.txt file
already shared conf file and yes possible to have 3 or 1 result
Can you plz help me how you fix the problem of log.txt file?
Have you fixed it or not
Sir , how can we choose the metal complexes ( own synthesized) as a ligand ..because it is new complexes..?
create its smiles first
Assalam alaikum Sir!
Thank you so much for amazing tutorials on Docking.
I have completed 3 steps successfully but I am not able to generate log.txt file. Please guide me how to generate log.txt file.
Watch both parts again it's too easy just recall grid values then put in text file in shared format ok
Yes Sir! I will follow instructions given by you. Thank you so much for your help. Stay blessed Sir!
@@iqrasajid1679 welcome
AOA sir very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?
waslam set max grid on all protein surface then see result and other way to check active site residue by I-TASSER
Sir homology modelling m bhi video bnye
done and look on I-TASSER
Very informative !!.. can we publish paper with autodoc vina results and in what type of journals?
Sir Vina K Folder me Jo Config Tzt file Ha
Ye Khuf se Create Ki Ha
yes
What is log.txt file? I couldnt get mine
Sir g ! log.txt file main likhna kiya hai??plz tell
Dear, Log file will be generated automatically by your script of code
Nice video sir.My pc configuration is i5, ram=4gp,hardisk=1 tera. Can I perform autodock in my pc with that configuration?
ofcourse u can
@@Prof.Dr.MuhammadNaveed Sir I have a lot of quary,for docking.
1. i want to dock epitope that shows hightest binding for HLA/HLA-DRB. So in that case which one i take as ligand and which one i take as protein
2.When i download HLA/HLA-DRB from protein data bank,where i found the HLA/HLA-DRB binding with ligand. So how can i prepare my HLA/HLA-DRB by removing the ligand?
3. When i download autodock tools it normally download on local disk.so may i cut it from local disk and take it into another folder??
@@fahimalamnobel4789 Dear, In case of HLA and Epitope, you will go for protein-protein docking.
You can simply remove the ligand by using discovery studio just like you remove water molecules.
Yes you can move it
any other query? feel free to ask.
@@Prof.Dr.MuhammadNaveed Sir if i follow the step by step of your docking lecture,than i can make the HLA/HLA-DBR and epitope docking properly??
@@fahimalamnobel4789 No. You have to do protein-protein docking. You can use CLUSPRO or HADDOCK. we will make a video on it soon InshaAllah.
Assalam Alaikum sir... Sir, I have downloaded vina but I did not get the executable file... I tried many times...
then might be you PC issue
Dr. M Naveed Sb. Aslam O Alaikum, I am following for learning docking. But i cant download autodock vina can you send me a link for that downloading . my ram is 8GM process
vina.scripps.edu/download.html
mgltools.scripps.edu/downloads
Wslam
Thank you Sir for crisp and clear explanation. i have one doubt (17:45 of video). Sir, what does 9 different files/energies of ligand means? Is it 9 different ligands which can bind to our target or 9 different active sites of target where same ligand can bind?
same ligand on 9 different positions of active site
@@Prof.Dr.MuhammadNaveed Thank you Sir!
Dear sir I am facing an error while choosing macromolecule in MGL tool 1.5.4 through python 'listed index out of range'. Can u please guide how to fix it.
Sir how to download auto dock please needed help
link avialable at part 1 of this lecture
How to solve parsing line problem during running docking ?
parsing line?
Dear Sir, you didn't mention anywhere how to prepare log.txt file, please share a screenshot of the contents of log.txt file. Thanks
mentioned
after following the same path way in the result part it ia showing vina is not readble your config file. Can any one suggest how to solve this problem?
I amhave tried almost 50 times but same resul. please suggest some thing.
Assalam.O.Alaikum! Respected Sir! Plz provide guidelines for proeins with DNA docking process....
watch video on patchdock
how to get this log.txt file??????
Sir ye cofigration file c disk mqi save ni ho rhi ?why
do save in vina folder in program file
AOA, Dr. Naveed how someone can pursue a PhD research in Molecular Docking?
waslam not truly in docking but can do research work in any drug or vaccine design up to in vivo and in vitro trial then seem good
@@Prof.Dr.MuhammadNaveed Sir can we talk on phone???? for a little discussion.........
AOA sir I hope that you are in good health and safe. Sir, your video tutorials on different topics of bioinformatics is very useful and informative. Sir, I just want to ask you that how can we perform autodock vina to identify/find vaccine candidate for covid 19?
Thank you and hope to hear from you soon!
docking is only one of the step in vaccine design and rest watch my lecture on drug design
@@Prof.Dr.MuhammadNaveed ok thank you sir. Sir, I have one more question that how can we tell from the docking results that our inhibitors compound of interest is inhibiting the protein such as SARS-CoV 2 proteins?
Please Guide me how can I compare putative docking sites of my quarry protein in different organisms
by manual docking with each organism conserved protein
Ok Sir Jaza kallah khair
Sir g kindly reply kar dian log.txt file main kiya likhna ?
We have to write down grid values in conf file. Log file will be generated automatically.
Hello sir, for the preparation of ligands for docking, is it requirement of removing heteroatoms like halogens? Because when I wanted to dock halogenated organic ligand with protein, autogrid is going on soomthly, but in autodock , there is a problem for finding halogens map.
Yes need to remove
@@Prof.Dr.MuhammadNaveed thank you so much.
Assalam.O.Alaikum Respected Sir! There is any tool or software available for comparison of putative docking sites of quarry protein in different organisms like Plants, Human, bacteria, fungi etc protozoa
yes can use this
This tutorial is command based, can you please make a video of manual docking? Like in command based you dont need to make GPF and DPF files
sure
Molecular Modeling Bhi Samjha Dayty Sir
watch my lecture on I-TESSER
Sir, while prepairing and conf.txt file and running according to your process, my system in Commend prom, showing error in conf.txt file or else not able to read.What could be the reason for it? kindly suggest.
put you conf file in vina folder of C derive
Sir, I am getting belloow problem: Kindly help me out
Input:
--receptor arg rigid part of the receptor (PDBQT)
--flex arg flexible side chains, if any (PDBQT)
--ligand arg ligand (PDBQT)
Search space (required):
--center_x arg X coordinate of the center
--center_y arg Y coordinate of the center
--center_z arg Z coordinate of the center
--size_x arg size in the X dimension (Angstroms)
--size_y arg size in the Y dimension (Angstroms)
--size_z arg size in the Z dimension (Angstroms)
Output (optional):
--out arg output models (PDBQT), the default is chosen based on
the ligand file name
--log arg optionally, write log file
Misc (optional):
--cpu arg the number of CPUs to use (the default is to try to
detect the number of CPUs or, failing that, use 1)
--seed arg explicit random seed
--exhaustiveness arg (=8) exhaustiveness of the global search (roughly
proportional to time): 1+
--num_modes arg (=9) maximum number of binding modes to generate
--energy_range arg (=3) maximum energy difference between the best binding
mode and the worst one displayed (kcal/mol)
Configuration file (optional):
--config arg the above options can be put here
Information (optional):
--help display usage summary
--help_advanced display usage summary with advanced options
--version display program version
C:\vina>
Thank you for the best explanation. Kindly, guide me about compound synergism.
could you elaborate your question in light of Bioinformatics and yes can check synergism by docking
great sir. par hamy receptor ligand complex hesay dikht ga? docked complex?
PayMol sy after docking
@@Prof.Dr.MuhammadNaveed thanks🤩
Thanks sir
Welcome
It is very useful lecture sir. I want to dock nanomicellis or nanoparticles with target proteins. Is it possible? How can I do?
Yes possible if go for full drug and for that you may go through these articles pubs.rsc.org/en/content/articlelanding/2013/ra/c3ra42534g/unauth#!divAbstract www.ncbi.nlm.nih.gov/pubmed/24088267
Thank you sir.
any student of sir naveed here? i need some help regarding autodoc vina.
Yes...! Teaching Assistant to Dr. Muhammad Naveed here....! If you have any query kindly contact me at 0323-6667667
Respected Professor, Thank you so much for such an informative video. I have a question and I need your valuable guides about it After command prompt config conf. txt -- log log.txt here what is log.txt.
By the way, I stuck at this point because the next stops r not working. secondly, in vina there is no log text. file
you have to create the log file in c derive of vina folder rather than on desktop
@@Prof.Dr.MuhammadNaveed Respected Professor, i tried so much but failed how i create log file ? If you have time please guide me i shall be very thankful to you
@@Prof.Dr.MuhammadNaveed i have the same question as well !!!
@@ihsanullah8140 i encountered the same problem then i sought out the way to fix it by manually creating log.txt file on desktop. Later on, i copied this file and paste in Vina folder.
@@zainabsheikh6307 is it working then?
Am beginner kuch ni smjh a rha flhal