I-TASSER | Protein 3D structure prediction | Results Analysis | Lecture 6 Part 3| Dr.Muhammad Naveed

I-Tasser Results Output Page Description In Details
#3DStrucutre #ProteinModelling #HomologyModelling

[@javeriaaltaf]

Thank you for describing everything. Your way of lecture delivery is impressive.

[@Prof.Dr.MuhammadNaveed]

pleasures

[@muhammadmukheed8594]

Sir Thank you for these informative lectures. Previously I think bioinformatics is very tough but after watching your lecture I find it very easy... Thank you.

[@ayeshamalik4679]

Sir your videos are informative for researchers and students also thankful to you

[@Prof.Dr.MuhammadNaveed]

pleasures

[@pawansharma8028]

Very precise and accurate explanation. Well done.

[@Prof.Dr.MuhammadNaveed]

pleasures

[@tahiraaslam4365]

Excellent 👍 Sir

[@Prof.Dr.MuhammadNaveed]

So nice of you

[@MayankSingh-uj6hi]

Sir aap really best ho thanks

[@Prof.Dr.MuhammadNaveed]

Thankyou so much

[@abubakarbashir7951]

I can see that you are doing a marvelous job, only that us that cannot hear your language are missing a lot. How I wish you will find way so that you can also go along with us. We will really appreciate that. Thank you, Sir.

[@Prof.Dr.MuhammadNaveed]

Thanks, dear for the compliment and in near future will deliver lecture in English

[@abubakarbashir7951]

@@Prof.Dr.MuhammadNaveed Thank you so much Dr for the positive response. I really appreciate that.

[@tahiraghulam2733]

Such a nice tutorial. full of knowledge.

[@Prof.Dr.MuhammadNaveed]

pleasures

[@user-bv7zd9xn2v]

Thanks for describing. Respected Sir, the active site predicted by I Teaser can be used for focused docking?

[@ahmedawan5909]

Sir I understand if rampage shows different values for same protein model in different species is due to differences in secondary structure

[@sarahnawaz6925]

Thank you sir,best video!

[@Prof.Dr.MuhammadNaveed]

welcome

[@bloom.ss67]

Thankyou sir. I needed this so much.

[@ahmedawan5909]

Please response to these questions also thank you so much for providing information regarding I tasser

[@ahmedawan5909]

Can Secondary structure of protein contains favoured region allowed regions in Rampage?

[@Prof.Dr.MuhammadNaveed]

yes ofcourse

[@ayeshamalik3030]

when we click on Enxyme comission number than enzyme name is open what does it mean in I TASSER ?

[@Prof.Dr.MuhammadNaveed]

It actually describes the class family and other features of enzymes based on chemical reactions innvolved.

[@ayeshamalik4679]

Sir I have question the statistics used to compare results in I tasser are c score z score and TM score when both values are maximum protein is accurate and reliable ?

[@Prof.Dr.MuhammadNaveed]

normally we use C-Score for best predicted model identification. Yes, the good values mean good accuracy and reliability

[@ayeshamalik3030]

in I Tasser what is purpose of enzyme comission number?

[@Prof.Dr.MuhammadNaveed]

The enzyme commission number basically is a specific number allotted to each enzyme showing its class and family and other characteristics

[@ahmedawan5909]

We know that secondary structure folded to make tertiary structure then why in I tasser secondary structure dont show differences when folded to 3D protein model and same protein model in i tasser for different species? And in Rampage secondary structure is different in same 3D protein models of different species so values different why?

[@ayeshamalik3030]

Aik question tha what are characterstics of 3D protein models? Are the protein model different in different species? if difference than explain and if same then remove from the thesis? in this question i am asking that can i remove just figure of protein models according to question?

[@Prof.Dr.MuhammadNaveed]

you mention all protein models in text but in figure just put those have different 3 D models ok

[@hassanmushtaq9234]

Excellent sir❤

[@Prof.Dr.MuhammadNaveed]

welcome

[@ayeshamalik3030]

If Protein models are same in different species through I TASSER then why RAMPAGE gives different values of favoured allowed and outlier region for same protein model in different species?

[@ahmedawan5909]

Can I tasser software be helpful to tell us differences in secondary structure of protein ?

[@Prof.Dr.MuhammadNaveed]

yes

[@ahmedawan5909]

Agar aik molecular marker sae protein structures construct krae by I tasser then protein models will be same for different species?

[@ayeshamalik3030]

Sir The Structure and Function of protein are characterstics of three D protein model?

[@Prof.Dr.MuhammadNaveed]

somehow, these are dependent on the structure

[@ayeshamalik4679]

It is necessary thar TM score and Z score are not mentioned in the statistics of I tasser

[@ahmedawan5909]

In I tasser secondary structure of protein is not changed and same 3D protein model for different species then suddenly in Rampage result how secondary structure of protein is changed for same 3D protein model in different species?

[@ayeshamalik3030]

in my data the C scores have less varaition and template homology PDB ID is same for different species and function is also same in different species Can i predict that protein models are structurally and functionally same in Different species?

[@anisasehar2220]

Can we use this scheme for mutated protein?? and can predict mutated protein function? of we need to make some changes.... one more thing is it possible to get the 3D structure of a specific protein DOmain???

[@Prof.Dr.MuhammadNaveed]

yes can do

[@decodingbio8114]

Sir please improve sound quality in start and at end when you face the camera during demonstration it was good Well effort Sir

[@Prof.Dr.MuhammadNaveed]

ok dear only in the last lecture faced this problem as mic off :) anyhow will check in next lecture.

[@ayeshamalik3030]

if protein models are same for different species in I TASSER? then why RAMPAGE gives different values of different species if protein models are same?

[@Prof.Dr.MuhammadNaveed]

RAMPAGE gives you the information about favored and unfavoured regions. That could be different in protein structures. There might be a difference in helix or turns or coils.

[@ahmedawan5909]

Why rampage gives different values for same protein model predicted by I tasser in different species?

[@Prof.Dr.MuhammadNaveed]

There might be difference in secondary structure

[@ahmedawan5909]

I tasser donot tell us differences in the secondary structure of protein and we assume protein model same due to no variation in C score and same template id but in rampage secondary structure of protein can be determined that contains favored allowed regions etc?

[@ahmedawan5909]

The ten different species have same protein models in I tasser then why same protein model for ten different species show different values in Rampage?

[@Prof.Dr.MuhammadNaveed]

There might be difference in secondary structure

[@harisjan6047]

Sir my protein amino acid is very long and I taser is unable to run it , is there any alternative tool available to I taser which can generate structure?

[@ayeshamalik3030]

In RAMPAGE the values of favoured and nonfavoured regions were diffferent in same protein models for different species?

[@Prof.Dr.MuhammadNaveed]

could not understand your query. Pleaese elborate your query at [e-mail]. Teaching assistant will reach you shortly

[@fahimalamnobel4789]

Sir in which format I-TASSER will give the result? Sir, will I get the result in educational mail or the institutional mail is a must for getting the result? Sir, I have another query. I want to use pymol for visualization may I use it in research purposes,i only found the edu pymol for free and it is not possible for use paid version, so can I use edu pymol for my research work or publication?

[@Prof.Dr.MuhammadNaveed]

dear result will be received in a web link in suggested email and when you click on it it will appear in web form. yes you can use pymol for research means

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed but sir in pymol site there is a clear indication that edu pymol cannot be used for research and publication.It can only be used for learning? But i am confused what to do.Thats why i am asking this?

[@Prof.Dr.MuhammadNaveed]

@@fahimalamnobel4789 you can used

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed Thank you very much, sir. Sir, I have another query that is when I use iedb for mhc1 binding,there I found the most probable allele for my selected epitopes. Further, I want to check the selected epitope and allele binding affinity(recheck or cross-check) by another online server, named EPISOPT(bio.med.ucm.es/episopt.html), recently I saw a paper, in there they recheck there epitope and allele binding affinity with that server. But the problem is I cannot enter into that link. Sir kindly help me I this regard or suggest me another server by which I can recheck my epitope and MHC 1(allele) binding affinity.

[@ayeshamalik3030]

different species C score template id same for all species A 0.91 B 0.90 C 0.93 D 0.96 E 0.91 F 0.93 G 0.94 H 0.89 I 0.94 J 0.92 This is i tasser results C score and template id same for different species . IS 3D Protein models same for different species according to values?

[@Prof.Dr.MuhammadNaveed]

send your query in detail at [e-mail]. Teaching assistant to Dr. Muhammad Naveed will reach you shortly.

[@ahmedawan5909]

If C score has no more variation and template is same for all species then we predicted that protein models are structurally same for all species?

[@Prof.Dr.MuhammadNaveed]

yes

[@ahmedawan5909]

If protein models of different species have same function then we expect that protein models are same?

[@ahmedawan5909]

If protein models are same for different species in I Tasser then why in Rampage software protein models shows different values for different species?

[@Prof.Dr.MuhammadNaveed]

there might be difference in secondary structure of protein.

[@ahmedawan5909]

Can I tasser tells us about the differences in secondary structure of protein? How we can estimated the differences in secondary structure of protein in ITasser?

[@ayeshamalik3030]

Can RAMPAGE software that is used for validation of protein can be performed with Same protein model in different species?

[@Prof.Dr.MuhammadNaveed]

yes, can be

[@ahmedawan5909]

If protein models of different species have same function then protein model is same for different species ? Please explain this I am confused?

[@ahmedawan5909]

If protein model of different species have same function then we expect that protein models are same?

[@Gautamkumar-om7im]

Can we use the predicted model by i tasser for docking purpose or we have further do something to the predicted model like, energy minimisation, Ramachandran plot prediction?sir please make a video on this topic.

[@Prof.Dr.MuhammadNaveed]

sure and you can go with predicted model

[@nidhijindal22]

SIR WHY PART 2 IS NOT AVAILABLE?

[@farihajavaid4653]

Aoa sir...when im downloading model file does not open...kindly tell me which software is used to visualize these models or to read pdb files...

[@Prof.Dr.MuhammadNaveed]

PyMol or discovery studio

[@farazkhan8713]

Sir, please make a video about molecular modelling of protein which lies in twilight zone using abintio method.

[@Prof.Dr.MuhammadNaveed]

sure, but I-TASER cited mostly in articles and made video on it

[@deepasreek5172]

Sir, the C-score value for my protein model1 was -4. Is it okay to use that model for further studies?

[@ayeshamalik3030]

if we construct protein structures with only one molecular marker by I TASSER then protein structures will be same in different species?

[@ayeshamalik3030]

if C score of different species are 0.91, 0.90, 0.93,0.96, 091,0.93, 0.94, 0.89, 0.94 and 0.92 and template id is same for all species then protein model will be same or different ? please explain this

[@Prof.Dr.MuhammadNaveed]

it depends upon the secondary structure

[@ahmedawan5909]

Is it possible that I tasser developed same protein models for different species?

[@ayeshamalik3030]

Can I Tasser tells about the Characterstics of 3D protein model? which part of I TASSER describes the 3D protein model Characterstics?

[@zainiiBee]

My ques is I used ITASSEr and TrRosetta both. Both showed diff models Should i go for ITASser ? The 1st predicted structure in ITASSEr needs to be validated through Ramachandrn plot? If so then my 1st predicted model gives allowed residues of 85%. What should i do?? Please guide . I need a complete guide as i am stuck

[@Prof.Dr.MuhammadNaveed]

go with I-Taser and refine score by glaxyrefine

[@zainiiBee]

@@Prof.Dr.MuhammadNaveed i did it. After refining when i chek again the quality was now down from 82% before refining to 69% after refining. Any suggestion please sir???

[@ayeshamalik3030]

Agar secondary structure of protein mae difference ho teo Rampage gives different values for same protein model in different species predicted by I TASSER?

[@chiragsoni6770]

Sir is everytime possible we will get top five models predicted by I-TASSER of query seq. ? Because I got only one model

[@Prof.Dr.MuhammadNaveed]

most of time possible to have 5 models but when sequence is unique or have less homology then possible to have 1 or 2 but if score is ok then you may use this

[@chiragsoni6770]

@@Prof.Dr.MuhammadNaveed I got C-score value of my predicted final model is 0.61 and got TM-score value that is 0.949 and Coverage of alignment is 1.000 to related PDB structure. So is my structure good or bad ? Can I use it for further protein-ligand docking process ?

[@ahmedawan5909]

The difference in secondary structure of protein could be observed in Rampage only in the form of different values in favored allowed region and outlier region?

[@simonparmar2458]

Sir, can you plz make a video on molecular docking.?

[@Prof.Dr.MuhammadNaveed]

kzbin.info/www/bejne/rl7ZqoB_qKihiZI

[@ayeshamalik3030]

if proteins models are same for different species in I-TASSER then we can validate the protein model by RAMPAGE if protein models are same?

[@Prof.Dr.MuhammadNaveed]

yes u have to validate and refine

[@ayeshamalik3030]

So For same protein model in different species and different protein models in Different species the values of favoured and nonfavoured region is always different?

[@ahmedawan5909]

Agar rampage values different show ho rhae hae in different species it means protein model are different in I tasser?

[@ahmedawan5909]

If protein models are same in I tasser for different species then in Rampage the values of favored nonfavoured region will not show too much difference?

[@ayeshamalik3030]

Can we estimate that protein models are different or same in different species in I- TASSER with he help of C score and template homology ID? IF C score has no variation and template id is same then protein models are same for different species?

[@ahmedawan5909]

My question is that if we have same protein models for different species in I tasser then validation by rampage give same values of favoured allowed regions in different species?

[@ayeshamalik4679]

What statistics are used in the ramachandran plot analysis is allowed region outlier region and favoured region are statistical ratios?

[@ayeshamalik3030]

In my result the C score of ten diffferent species are 0.91,0.90, 0.93, 0.96,0.91,0.93,0.91,0.96,0.92,0.89 and template model is cryo -EM strcutre of stringent respnose factor REIA bound to ErmCL- Stallled ribosome complex in all ten species is protein model same for ten different species?

[@Prof.Dr.MuhammadNaveed]

yes

[@hitkarshkushwaha2434]

👌👌👌

[@Prof.Dr.MuhammadNaveed]

Pleasures and welcome dear

[@ayeshamalik4679]

The value of Z score 3.63 is good value?

[@Prof.Dr.MuhammadNaveed]

depends upon the comparison with other values. If it is the highest, than it is.

[@ayeshamalik3030]

if the protein models have no difference in different species by I TASSER? then it is possible to be validated by RAMPAGE?

[@ayeshamalik4679]

If structure and function is Same and cellular component is different than 3D protein model will be same ?

[@ayeshamalik3030]

if protein models are same in different species through I- TASSSER can we validate the same protein models of different species through RAMPAGE?

[@Prof.Dr.MuhammadNaveed]

yes you can validate

[@hassanmushtaq9234]

Sir jo proteins bre hte hain more than 1500 ... uski prediction kese krain gy?

[@Prof.Dr.MuhammadNaveed]

then need to use a manual method of modeling as by using MODELLER

[@ayeshamalik3030]

Sir agar protein models same ho for different species in I TASSER then after validation by RAMPAGE there is no much difference in the values of Favoured allowed region ?

[@ahmedawan5909]

Sir agar favoured region and allowed region and outlier region kae values mae itna difference nhe Ara ha it means protein model are same for different species? The favoured regions values are 88 87 85 84 83 81 and allowed region values are 7 8 9 10 11 and disallowed have 0 0 0 4 2 etc? Is protein models almost same in different species?

[@Prof.Dr.MuhammadNaveed]

yes same

[@ahmedawan5909]

Sir these values also have no more difference?

[@Prof.Dr.MuhammadNaveed]

@@ahmedawan5909 same

[@ahmedawan5909]

Sir merae data favoured allowed region mae values mae itna difference nhe hae na we considered that no variation ?

[@ayeshamalik4679]

I have also question and commented on the clustal W and phylogenetics lecture please reply to this question also

[@ahmedawan5909]

Secondary structure of protein kae andar jo differences aataee hae wo just rampage mae pta chalta hae KIA?

[@ayeshamalik4679]

Is it possible that tasser develop same model for different species ?

[@Prof.Dr.MuhammadNaveed]

yes possible if query sequence have less variations

[@ayeshamalik3030]

In Callicarpa and Tectona species i have noticed from the result that in Callicarpa the cellular component is cytosol while in Tectona the cellular component is chloroplast while rest biological and molecular function same so we can say that different model due to minute sequence variation?

[@ahmedawan5909]

Agar hum same protein models ko validate krae gaieee rampagae sae teo they always give same values of favoured allowed regions

[@Prof.Dr.MuhammadNaveed]

you are telling something or asking?

[@ahmedawan5909]

Asking

[@Prof.Dr.MuhammadNaveed]

@@ahmedawan5909 contct us through phone so we may guide you properly

[@ahmedawan5909]

Sir ap mujay email per bta daiaee my phone is not working properly

[@ayeshamalik4679]

Sir statistics of I tasser mae.Kia mention kr sakataee just C score?

[@Prof.Dr.MuhammadNaveed]

No each score in I-Tasser is statistics-based. Tm Score, Z-Score, C-Score

[@ahmedawan5909]

How we can estimated that protein model is same or different in I tasser for different species what's the reason?

[@ahmedawan5909]

How can be estimated that protein models for different species in I tasser are different or same in different species?

[@ahmedawan5909]

Can i tasser and Rampage software both can tell us differences in the Secondary structure of protein?

[@ayeshamalik4679]

I am confuse which statistics used in ramachandran plots by rampage?

[@ahmedawan5909]

If the template is same for all species in I tasser then protein model will be same?

[@fahimalamnobel4789]

Sir plz make a video on Ramachandran plot and analyze in RAMPAGE and Molecular dynamics after protein-ligand docking to analyze the binding quality in AMBER software, or another well-known software.

[@Prof.Dr.MuhammadNaveed]

sure dear will do thanks

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed Sir another problem i am facing in 3D modeling .Sir i have n't any educaional mail.What should i do then??

[@Prof.Dr.MuhammadNaveed]

​@@fahimalamnobel4789 dear use email ID any of your friend as only results link will be send on that email so ask any teacher or friend otherway use MODELLER offline tool

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed Sir MODELLER tool can be download by free from online?

[@Prof.Dr.MuhammadNaveed]

Dear@@fahimalamnobel4789, Yes it can be.

[@ayeshamalik4679]

If the Z score is 2, 3, 4,8,9 for different species then we said that score is best?

[@ayeshamalik3030]

Can we validate the same protein models in different species through RAMPAGE?

[@Prof.Dr.MuhammadNaveed]

yes

[@sonamgupta1062]

sir agr 3D str. mai Z score less than 1 aa rha ho toh kya krna cahiye

[@sarakhazeema6629]

How to predict the disease causing mutation of a protein through I-TASSER sir? Please answer

[@Prof.Dr.MuhammadNaveed]

not by I-Tasser but can compare structures

[@syedaanam1732]

Which tool/software to be used for the visualization of protein structure downloaded as pdb file?

[@Prof.Dr.MuhammadNaveed]

Discovery studio or JMol

[@ahmedawan5909]

Is it possible that I tasser develops no difference in protein model for different species?

[@Prof.Dr.MuhammadNaveed]

Already replied many times

[@ahmedawan5909]

Agar rbcl protein sae all structures construct Krae by i tasser in different species then protein model will be different or same?

[@ayeshamalik4679]

The change in the cellular component of 3D protein model but function same then we predict protein model are different?

[@Prof.Dr.MuhammadNaveed]

might be

[@fahimalamnobel4789]

Sir, I have done all the things perfectly. Alhamdulillah. But sir I am now a little bit confused about the structure refinement and energy minimization. Is the two things do the same work? I am also confused that which work i performed first, energy minimization or refinement??

[@Prof.Dr.MuhammadNaveed]

Both different as structure refinement relevant to structure validation and energy minimization is related to molecule interaction

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed Sir when i modeled my protein structure i validate it through ramachandran plot,so i get 88% in favoured region but sir after i refined my structure by 3d refine server and then energy minimization is done . After that i again check it by ramachandran plot.But after refinement and energy minimization my proteins favoured region get decreased in 85%.What is the region of that. ?

[@Prof.Dr.MuhammadNaveed]

@@fahimalamnobel4789 so that means other 15 % is now in unfavoured region

[@fahimalamnobel4789]

@@Prof.Dr.MuhammadNaveed Sorry sir 83.1%,so the structure is valid in that percentage?? Another think is written in procheck server that is "You have no END tag. You must have 1" .I dont understand this sentence. The sentence shows after refinement and energy minimization of my structure. And in some structure this sentence is also written before and after the refinement and energy minimization of the protein.

[@Prof.Dr.MuhammadNaveed]

@@fahimalamnobel4789 yes if it is the standard mentioned in the tool page

[@ayeshamalik3030]

Favored region Allowed region Outlier region 88 8 2 81 10 7 85 9 4 87 9 2 85 13 0 85 13 0 88 8 2 84 13 1 83 13 2 84 11 3 This is result of Rampage validation of same protein model for different species is values different in Rampage results when we estimate that protein models are same for different species?

[@Prof.Dr.MuhammadNaveed]

Your query is not clear. Please elaborate your query art [e-mail]. Teaching assistant to Dr. Muhammad Naveed will reach you shortly.

[@ahmedawan5909]

Please answer to this question it is urgent question thanks

[@zainabhasan1020]

through which software can we download these models

[@Prof.Dr.MuhammadNaveed]

you can generate these models using I-Tasser

[@Prof.Dr.MuhammadNaveed]

install Discover studio or JMol or PyMol for downloading and visualization of Models

[@ayeshamalik3030]

SIr i want to ask that Callicarpa species has 0.91 C score and Tectona has 0.90 so is the different model is different for these two species? if we estimat e that Different C score leads to different 3D protein model

[@Prof.Dr.MuhammadNaveed]

their score not much different so model might also same

[@ayeshamalik3030]

In my data active site is different in different species then model will be different?

[@ahmedawan5909]

Is it possible that same protein models for different species in I tasser gives different values of favoured allowed region in rampage what's the reason?

[@Prof.Dr.MuhammadNaveed]

Yes possible as might have difference in secondary structure

[@ahmedawan5909]

In I tasser if amino acid sequence not changed then structure of 3D protein models is also same?

[@Prof.Dr.MuhammadNaveed]

yes

[@ahmedawan5909]

Agar aik hae protein sae models construct krae for different species then protein model will be same or different?

[@ahmedawan5909]

If template and function of protein models are same in different species then we predicted that protein models are same in different species?

[@ahmedawan5909]

If protein models are same for different species in I tasser then in Rampage we validate the protein model of all species?