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.
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.
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?
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?
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?
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 ?
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?
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?
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?
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?
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?
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?
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?
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?
Agar secondary structure of protein mae difference ho teo Rampage gives different values for same protein model in different species predicted by I TASSER?
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?
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?
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.
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?
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
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 ?
if i have two protein model and C score value for 1 is 0.90 and second is 0.91 and TM score for 1 is 0.896 and second is 0.892. THe template model is same for both 1 and 2 . then protein model will be same or different? please explain this?
Assalum u likum agar journal mae mention ho kae for colour priniting charges will be paid then journal will asks after acceptance that which type of priniting do you want?
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?
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?
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
The result of third species by I Tasser shows the C- score 0.93 and in my result function is same template is same can i predict that different protein model of different species based on C score . My C- score values are 0.90, 0.91 and 0.93 for different plant species?
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.
@@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
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???
In my data the template for two different species are same but cellular component of two different species are changed can I predict two protein models are different ?
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.
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 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???
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
@@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 ?
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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.
Thankyou sir. I needed this so much.
Thank you for describing everything. Your way of lecture delivery is impressive.
pleasures
Sir your videos are informative for researchers and students also thankful to you
pleasures
Please response to these questions also thank you so much for providing information regarding I tasser
Such a nice tutorial. full of knowledge.
pleasures
Sir aap really best ho thanks
Thankyou so much
Very precise and accurate explanation. Well done.
pleasures
Thank you sir,best video!
welcome
Excellent 👍 Sir
So nice of you
Thanks for describing. Respected Sir, the active site predicted by I Teaser can be used for focused docking?
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.
Thanks, dear for the compliment and in near future will deliver lecture in English
@@Prof.Dr.MuhammadNaveed Thank you so much Dr for the positive response. I really appreciate that.
Sir please improve sound quality in start and at end when you face the camera
during demonstration it was good
Well effort Sir
ok dear only in the last lecture faced this problem as mic off :) anyhow will check in next lecture.
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?
What statistics are used in the ramachandran plot analysis is allowed region outlier region and favoured region are statistical ratios?
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?
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?
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
?
👌👌👌
Pleasures and welcome dear
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?
Can I Tasser tells about the Characterstics of 3D protein model? which part of I TASSER describes the 3D protein model Characterstics?
Sir I understand if rampage shows different values for same protein model in different species is due to differences in secondary structure
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?
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?
Excellent sir❤
welcome
Secondary structure of protein kae andar jo differences aataee hae wo just rampage mae pta chalta hae KIA?
I have also question and commented on the clustal W and phylogenetics lecture please reply to this question also
Can i tasser and Rampage software both can tell us differences in the Secondary structure of protein?
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?
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?
Agar aik molecular marker sae protein structures construct krae by I tasser then protein models will be same for different species?
How can be estimated that protein models for different species in I tasser are different or same in different species?
if the protein models have no difference in different species by I TASSER? then it is possible to be validated by RAMPAGE?
In my data active site is different in different species then model will be different?
Agar rampage values different show ho rhae hae in different species it means protein model are different in I tasser?
Sir, the C-score value for my protein model1 was -4. Is it okay to use that model for further studies?
How we can estimated that protein model is same or different in I tasser for different species what's the reason?
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?
if we construct protein structures with only one molecular marker by I TASSER then protein structures will be same in different species?
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?
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?
Agar secondary structure of protein mae difference ho teo Rampage gives different values for same protein model in different species predicted by I TASSER?
If structure and function is Same and cellular component is different than 3D protein model will be same ?
I am confuse which statistics used in ramachandran plots by rampage?
If the template is same for all species in I tasser then protein model will be same?
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?
If protein models of different species have same function then protein model is same for different species ? Please explain this I am confused?
If protein model of different species have same function then we expect that protein models are same?
sir agr 3D str. mai Z score less than 1 aa rha ho toh kya krna cahiye
It is necessary thar TM score and Z score are not mentioned in the statistics of I tasser
SIR WHY PART 2 IS NOT AVAILABLE?
Is it possible that I tasser developed same protein models for different species?
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?
If the Z score is 2, 3, 4,8,9 for different species then we said that score is best?
Sir, please make a video about molecular modelling of protein which lies in twilight zone using abintio method.
sure, but I-TASER cited mostly in articles and made video on it
In RAMPAGE the values of favoured and nonfavoured regions were diffferent in same protein models for different species?
could not understand your query. Pleaese elborate your query at aqibmirza67@gmail.com. Teaching assistant will reach you shortly
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...
PyMol or discovery studio
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.
sure and you can go with predicted model
Which tool/software to be used for the visualization of protein structure downloaded as pdb file?
Discovery studio or JMol
Sir, can you plz make a video on molecular docking.?
ruclips.net/video/x-vyMIsCnS0/видео.html
when we click on Enxyme comission number than enzyme name is open what does it mean in I TASSER ?
It actually describes the class family and other features of enzymes based on chemical reactions innvolved.
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?
Yes possible as might have difference in secondary structure
Can RAMPAGE software that is used for validation of protein can be performed with Same protein model in different species?
yes, can be
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
it depends upon the secondary structure
The change in the cellular component of 3D protein model but function same then we predict protein model are different?
might be
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 ?
normally we use C-Score for best predicted model identification. Yes, the good values mean good accuracy and reliability
if i have two protein model and C score value for 1 is 0.90 and second is 0.91 and TM score for 1 is 0.896 and second is 0.892. THe template model is same for both 1 and 2 . then protein model will be same or different? please explain this?
If template is the same then pick a model with C score 0.91
Assalum u likum agar journal mae mention ho kae for colour priniting charges will be paid then journal will asks after acceptance that which type of priniting do you want?
watch article submission video and comment there and yes then need to paid at acceptance
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?
yes u have to validate and refine
Sir The Structure and Function of protein are characterstics of three D protein model?
somehow, these are dependent on the structure
Please answer to this question it is urgent question thanks
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?
yes
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?
you mention all protein models in text but in figure just put those have different 3 D models ok
if the active site of two different species contain different enzyme but function is same in different species then protein model will be same ?
active site present in enzyme and if same then model also same
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
their score not much different so model might also same
Why rampage gives different values for same protein model predicted by I tasser in different species?
There might be difference in secondary structure
The result of third species by I Tasser shows the C- score 0.93 and in my result function is same template is same can i predict that different protein model of different species based on C score . My C- score values are 0.90, 0.91 and 0.93 for different plant species?
no all same as very minor change and have same template
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?
There might be difference in secondary structure
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.
sure dear will do thanks
@@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??
@@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
@@Prof.Dr.MuhammadNaveed Sir MODELLER tool can be download by free from online?
Dear@@fahimalamnobel4789, Yes it can be.
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???
yes can do
In my data the template for two different species are same but cellular component of two different species are changed can I predict two protein models are different ?
yes you can use it differently at function level but same at structural level
Can Secondary structure of protein contains favoured region allowed regions in Rampage?
yes ofcourse
If protein models are same for different species in I Tasser then why in Rampage software protein models shows different values for different species?
there might be difference in secondary structure of protein.
Can I tasser software be helpful to tell us differences in secondary structure of protein ?
yes
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?
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.
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
go with I-Taser and refine score by glaxyrefine
@@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???
As in i tasser Z score greater than 1 considered to be good alignment so value of Z score 3.63, 3.65, 3.65 is good value?
yes sure
if protein models are same in different species through I- TASSSER can we validate the same protein models of different species through RAMPAGE?
yes you can validate
in I Tasser what is purpose of enzyme comission number?
The enzyme commission number basically is a specific number allotted to each enzyme showing its class and family and other characteristics
Active site is different but function of protein is same in different species then model will be same?
possible
Can we validate the same protein models in different species through RAMPAGE?
yes
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?
yes
If protein models of different species have same function then we expect that protein models are same?
In I tasser how we can estimate that our protein model for different species are same or different ? Please explain this?
on the basis of C score and template homology PDB ID
Which value tell us that protein model is different or same in I tasser?
C score of predicted 5 models
Sir jo proteins bre hte hain more than 1500 ... uski prediction kese krain gy?
then need to use a manual method of modeling as by using MODELLER
Ok so when we mention statistics in thesis then we mention C score Z score.and T score of I tasser?
C score
Sir is everytime possible we will get top five models predicted by I-TASSER of query seq. ? Because I got only one model
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
@@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 ?
Sir statistics of I tasser mae.Kia mention kr sakataee just C score?
No each score in I-Tasser is statistics-based. Tm Score, Z-Score, C-Score
How to predict the disease causing mutation of a protein through I-TASSER sir? Please answer
not by I-Tasser but can compare structures
Is it possible that tasser develop same model for different species ?
yes possible if query sequence have less variations