Molecular Dynamic Simulations | Drug Interaction Analysis | CADD Step 3 | iMODS | SwissDock | Lec 35

SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule.
S3DB, a database of manually curated target and ligand structures, inspired by the Ligand-Protein Database.
SwissDock is based on the docking software EADock DSS, whose algorithm consists of the following steps:
many binding modes are generated either in a box (local docking) or in the vicinity of all target cavities (blind docking).
simultaneously, their CHARMM energies are estimated on a grid.
the binding modes with the most favorable energies are evaluated with FACTS, and clustered.
the most favorable clusters can be visualized online and downloaded on your computer.
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at imods.chaconlab....
About Dr. Muhammad Naveed
Dr. Muhammad Naveed obtained PhD degree in Biotechnology (Genomics & Bioinformatics) from QAU, Islamabad with distinction. He has won PhD indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research from University of Ghent, Belgium. HEC awarded best PhD (IRSIP) Scholar of the year 2013 & QAU honoured him as “Distinguished Alumni” in 2017. He is doing research in Bioinformatics & Molecular Biotechnology. He has supervised 25 MSc., 30 MPhil. & 01 PhDs. He has published 51 research articles, 01 book and 03 book chapters. He has been awarded distinguished “Researcher of the Years (2016, 2018 & 2019)” by UoG and UCP.
#MDSimulations #iMODS #SwissDock

[@faizaghaffar1874]

Thank you so much sir, I'm really introvert this is the first time in my life that I'm commenting on any video. But, really wanna thank you. All of your videos made my project so easy that I got full marks and all worked so well. I performed complete CADD just through your videos. Really appreciate your great work 😊

[@fomiashahzadi7336]

Sir thanks for sharing knowledge..Sir kindly make videos on md simulation through Gromacs, Amber or NAMD..Although there are lots of videos on KZbin..but your teaching method is too good..So, it's my humble request Sir plz

[@fatimanoor5424]

Excellent..

[@Prof.Dr.MuhammadNaveed]

Glad it was helpful!

[@ilyasahmed7063]

Please tell how to open Swiss dock file in UCFF chimera?

[@JAIPRAKASH-zv8pg]

Sir pls help me ……my cluster file is not opening by chimera pls help me sir how to open this

[@rehanakhan7362]

Aslam o Alikum, Sir MA iMode ko stimulation analysis KY lye try kr rhi lakn nah chal rha kya kro. Please reply me.

[@hicicindehic6248]

you r the best

[@Prof.Dr.MuhammadNaveed]

pleasures

[@ayeshayasmin2931]

Aoa Sir I have done simulation with same protein but different ligands but problem is that results are same for all Ligands why??

[@zariniftekhar6866]

I perfpermed this molecular dynamics simulations and I used my complex, but not that the way you performed in Chimera sir, I perfoermd in pyrx and discovery studio, from.there I got my ligand-protein complex file. And I uploaded here. I got the same results in iMODS, but sir after this how to check the tgz file, and this is all about molecular dynamics simulations or any further step is there in this? Please guide me sir.

[@Prof.Dr.MuhammadNaveed]

for basic this is all but for more improvement need GROMACS

[@lifesciencedecoded]

Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga..... Sir plz doubt clear kar dijiye .... Usually water active site ko distort krta h interaction ke time, tbhi hum water molecules ko remove karte hain , but jab hum koi medicine/ligand create kar lenge to wo to phir body ke inside receptor protein main water hone se interaction hi nahi hone dega natural condition main..... Plz clear the doubt of my question sir .....

[@Prof.Dr.MuhammadNaveed]

they cope with many other interaction in body

[@hamzasohail3110]

sir yeh simulation protein-protein k liye bhe use ki ja skti?

[@harispremiumstore4181]

Sir which one is best for molecular docking autodock or swissdocking?

[@sanjaisrao484]

Sir I upload docked complex of my protein model..In B factor pdb graph is not showing , only NMA graph is there

[@Prof.Dr.MuhammadNaveed]

Run again

[@lifesciencedecoded]

As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?

[@Prof.Dr.MuhammadNaveed]

docking not possible in natural by you as this happened by nature but we opt all condition in dry lab to get natural results

[@lifesciencedecoded]

Thank you sir

[@koushiksarker1977]

Why IMODS server is not opening anymore? Can anyone suggest a better option?

[@raozubairkhaliq9092]

Sir could you please name some simulation tools which I can use in publications (with acceptable certainties) other than GROMAC (because I don’t know how to use Unix OS)?

[@Prof.Dr.MuhammadNaveed]

simlab

[@mohammadabdullah8584]

thanks for sharing such quick method for beginners , Sir in case if we are doing docking via MOE , then how can we upload the complex file on iMODS. Kindly guide in that perspective

[@Prof.Dr.MuhammadNaveed]

do as did for vina

[@alqurantheguideroflife3270]

Sir!How to open prediction file into UCSF chimera ?I have downloaded r install chimera but unable to open this prediction file

[@Prof.Dr.MuhammadNaveed]

follow as i did

[@sabreenaalam4976]

Sir, I have uploaded my pdb file of the receptor-vaccine docked complex on imod and got my result in one day. However, after one day the link of the result is showing site cannot be reached. I had to upload the pdb file again.The result is not coming yet since three days. The Imod job id is still running. What should I do? How much more time will it take for the results to come? also why is it taking more days now to give the result???

[@Prof.Dr.MuhammadNaveed]

I think due to overload so need to do again after some days

[@sabreenaalam4976]

@@Prof.Dr.MuhammadNaveed Thank you Sir for your reply.

[@zariniftekhar6866]

Sir, For Antibody Engineering please give lecture on this and online tools to perform antibody engineering.

[@Prof.Dr.MuhammadNaveed]

noted

[@zariniftekhar6866]

@@Prof.Dr.MuhammadNaveed Thank you so much sir for your reply.

[@jamesakash874]

Does Gromac and AMBER give better MD simulation result compared to Imod?

[@Prof.Dr.MuhammadNaveed]

yes definitely but here used online tool for beginners

[@user-yy1ow5xp6t]

Sir.. why imods is not working these days..

[@alqurantheguideroflife3270]

Sir! If the result of Pbd and NMD is not similar.all other result are good Then what I need to do?

[@Prof.Dr.MuhammadNaveed]

then you go ahead

[@saimamalik8115]

Sir docking MOE pe best nahe hai kia? Manual process hai wo zaida acceptable hoga thesis me?? MOE pe docking karai please, and gromacs pe m.d simulations

[@Prof.Dr.MuhammadNaveed]

yes noted but here use online tools which are well cited

[@saimamalik8115]

@@Prof.Dr.MuhammadNaveed sir auto dock vina ka koi easy way nahe hai? Agr hai tu please os pe ek lecturer krwai....

[@shahidcapital36]

A.o.a sir g ham na docking pyrx k through ki hy us men docked complex kasa save how gay

[@basyalpalpa5680]

thanks you very much sir

[@Prof.Dr.MuhammadNaveed]

All the best

[@sachindhawale2134]

Dear sir, when we upload the protein ligand complex, in results it doesn't show separate markers.?

[@Prof.Dr.MuhammadNaveed]

do check complex first then upload

[@hasmita7916]

Sir kindly tell any substitute tool for imod?

[@shakilcuchem]

Can i use this in thesis ?

[@dr.rimshariaz4688]

Sir mene simulation ki hy. But graph me pdb ki black line show ni hoti meri ksi b simulation me. Just red lines show ho rae hain... Kindly guide me k wo show kyu ni ho rae?

[@Prof.Dr.MuhammadNaveed]

use screenshot of original

[@deepjyotikalita9048]

sir how did you open the the seed1.crd file in chimera. I am not able to open it .It is showing to choose file type

[@Prof.Dr.MuhammadNaveed]

then your PC error

[@dr.abhaynandasrivastava951]

@@Prof.Dr.MuhammadNaveed Hello Sir, This is nice presentation. I am facing problem in opening seed1.crd file in chimera. If this is PC error, how to remove this, sir?

[@deepikadwivedi6107]

Hello sir, the presentation is really good. I have one query. I performed the same protocol that you shared here for IMOD. but somehow, I failed somewhere, I couldn't see the two peaks in the distance profile and B-factor. It would be so great if you could help me with this.

[@Prof.Dr.MuhammadNaveed]

then first check you docked complex interactions

[@deepikadwivedi6107]

@@Prof.Dr.MuhammadNaveed i have checked.. but still it's not working

[@bhagatsingh6345]

Sir any bioinformatics tool specific for promoter analysis of fungus

[@Prof.Dr.MuhammadNaveed]

many but you may follow this kzbin.info/www/bejne/gnTCkIOJi9idrtk

[@fatimanoor5424]

Sir predicted file direct chimera pr open ni ho ri... Seed1 download kr k jab file chimera pr open ki jati hy to file type select krny ka option ata hy.. Vahan sy crd file jo k seed 1 ki hy ..is k liy konc file type select ki jy?

[@Prof.Dr.MuhammadNaveed]

pdb or follow as i did

[@farhanzafar1418]

very helpful

[@Prof.Dr.MuhammadNaveed]

Glad to hear that

[@iqranoor5730]

sir ap ny Jo Jo step btya unko fellow kia imod k result aa raha graph but Jo first page pa protein k structure hai vo ni aa raha ...plzz guid kar dy

[@Prof.Dr.MuhammadNaveed]

run again

[@apnagaonapnadesh5842]

Sir iMOD surver show error massage when I uploaded protein ligand complex downloaded from SWISS DOCK. How to solve this problem Plz replies

[@Prof.Dr.MuhammadNaveed]

link down and wait to be active

[@malaikaanwar951]

sir swissdock shows that i have a protein of more than 15000 atoms so i should truncate my protein although there is no water molecule and extra ligands . what does it mean and what should i do?

[@literallymevideos]

remove the unnecessary chains from protein.

[@madhvikumarisinha7960]

How You open the Seed.1.crd in Chimera??? Kindly tell me, please..

[@Prof.Dr.MuhammadNaveed]

follow lecture

[@lifesciencedecoded]

Tq sir

[@mriganka7331]

Sir, whenever uploaded PDB file in iMOD server, everytime shows not valid pdb file, but the pdb file is ok. Would you please help me on it and is there any issue on the server, because such type of pdb file is shown the result earlier in the iMOD server.

[@Prof.Dr.MuhammadNaveed]

link down

[@mriganka7331]

@@Prof.Dr.MuhammadNaveed sir, please make a video on MD simulation (web server based like simlab). Thanks

[@ritwickbhattacharya7924]

Sir, How you predicted that seed 1 has the lowest energy. Waiting for your reply Sir

[@Prof.Dr.MuhammadNaveed]

based on results of complex

[@sachindhawale2134]

In other MD simulations, they performed on ns , simulation time. What about imod?

[@Prof.Dr.MuhammadNaveed]

algorithm design on standard ns

[@sachindhawale2134]

@@Prof.Dr.MuhammadNaveed Approximately how many ns?

[@pankajombase2856]

Whatever result we r getting from IMODS can we publish in research paper

[@Prof.Dr.MuhammadNaveed]

sure

[@manojdhameja4212]

Sir. Can we perform MD Simulation when inhibitor is non-competitive in nature ?

[@manojdhameja4212]

And kindly elaborate on the discussion about the results of MD simulation (this video).

[@Prof.Dr.MuhammadNaveed]

yes and sure will do in coming lectures

[@pankajombase2856]

Which one is better for md simulation vmd/NAMD or Gromac or online server ( Imod)

[@Prof.Dr.MuhammadNaveed]

GROMACS

[@rahulkumarvishwakarma6615]

Chimera is unable to open the seed crd file , what should I have to do??

[@Prof.Dr.MuhammadNaveed]

server down

[@manojdhameja4212]

Sir could you please provide literature of yours where you had shown md simulations ?

[@Prof.Dr.MuhammadNaveed]

literature ?

[@manojdhameja4212]

@@Prof.Dr.MuhammadNaveed yes sir

[@muhammadshahab1421]

And how we find residuals interaction of imod simulation.

[@Prof.Dr.MuhammadNaveed]

by graphs can analyze

[@muhammadshahab1421]

Sir can we put imod simulation in our manuscript if yes please share manuscript.

[@Prof.Dr.MuhammadNaveed]

yes you can and literature available on iMOD homepage

[@shariz005]

The link is down, is there another link ?

[@Prof.Dr.MuhammadNaveed]

no dear

[@informationtechnologywithu3783]

sir from where did you inference target ?? from step 2

[@Prof.Dr.MuhammadNaveed]

on the basis of ligand

[@informationtechnologywithu3783]

oky sir thankuh, sir please guide how to open seed crd file using chimera

[@lifesciencedecoded]

Sir what is the best docking software ?

[@Prof.Dr.MuhammadNaveed]

autodock vina

[@lifesciencedecoded]

Thank you sir

[@dr.rimshariaz4688]

Sir kindly share any paper from which i can see how to properly interpret it...

[@Prof.Dr.MuhammadNaveed]

Sars cov2 vaccine design by Muhammad Naveed search from google

[@AN-xb5td]

👍

[@siyabkhan110]

is simulation required super Computer?

[@Prof.Dr.MuhammadNaveed]

not all

[@siyabkhan110]

I used imode and it show that there is no b factors in my molecule

[@Prof.Dr.MuhammadNaveed]

run again to confirm

[@aman-fx6iz]

that dont work

[@janithjk4033]

Can you please do this in eglish or add English subtitles 🙏

[@Prof.Dr.MuhammadNaveed]

sure, will add subtitles

[@sarahnawaz6925]

Unable to open seed file ,please help sir

[@Prof.Dr.MuhammadNaveed]

do try again

[@rashamoustafa427]

Great but talking english clear in not quick 😊🎉🎉🎉🎉

[@swetajoshi3979]

Sir how to find traget

[@Prof.Dr.MuhammadNaveed]

on the basis of ligand

[@MuhammadAsad-cf5vi]

IMods Is not working sir and not giving results

[@Prof.Dr.MuhammadNaveed]

server down

[@GeneMania2024]

Sir,I have completed docking using Patch dock but imods showing error.What should I do?

[@Prof.Dr.MuhammadNaveed]

do with autodock then imods