Thanks for this effective tutorial. It’s very much elaborative to understand the overall process. I have one confusion. How will I understand which residues are missing? Would you please elaborate the process of identifying missing residues.
Nicely explained. But I want to ask what if I have selected only a single template? what command should I use? That time also I have to use model-multiple? I followed each step carefully but still, it shows an error while running the final command.
use similar steps ... but instead of model-multiple file u have to use model-defult.py file u can get that from this folder C:\Program Files\Modeller9.24\examples\automodel\model-default.py
Sir, loop refinement is or is not mandatory? Say, I have got good folded model unlike your tutorial then could I skip loop refinement part or should I go for loop refinement?
Thank you so much for the youtube video. Please my question is I am trying to find the missing residue but it use to tell me cannot find the MISSING, What should I do? My second question is that in my PDB Target sequence there are some missing amino acid what should I do with the gap or missing amino acid
if u having an issue with ur protein, u need to rebuild protein using any homology modeling tool, and u can use the model autodock. If u use the build protein model u can skp repair missing atom step in atudock.
Hello Sir, your previous videos were also very helpful for me to do docking, but in this part I am facing some problems, How shall I rectify them ???? As I performed the exact steps shown in both video. It would be grateful sir if you can help.
Great explanation, but i got error while running comand line . Actually the templates that I'm using don't have pdb format. In RCSB ,pdb format download option was not available so I downloaded the templates from pdb like zip file format. When I unzip them, there were 3 files for each protein (file name: pdb bundle 1 to pdb bundle 3 ) . I don't have any idea which pdb file for each protein is correct.
Sir your presentation was awesome. But I have 2 questions. 1. Why dope score always negative? 2. Why lowest dope score indicates better quality of modeled protein structure? Thanks in advance.
Professor what if we use 2 template and secondone have 2 chains(A,B) and both the chain is involved in alignment generation by ClustalΩ so when we convert this ClustalΩ fasta alignment file into ali format so we consider the residue range till B chain endedone ? (>P1;7dwmA structureX:7dwm.pdb:2:A:+235 here the end residue consider chain A or B)and in model_mult.py how I can put the chain B.
if we take resoultion factor and r value from crystalline structure which is already available in PDB, then why we are doing homology modeling?......model is already done.
Some sequence are missing my homology model. For example my protein has 642 amino acid sequence but after modelling i saw 636 amino acid in pymol..I did everything accurately....i did loop optimization also...but result is same.would you like to explain it to me plesse?
How to do modelling of trimeric proteins (multichain ) as in py file for multichain modelling we can do till 2 models one. If I am editing the .py for trimeric one by including s3 , it's giving syntax error . I edited alignment file too by putting/ . What are all the methods to do multichain , multitemplate modelling ? What should we do for transmembrane region of protein ?
Good evening everyone, I need your help. I have a database of molecules in the form of an SDF file and I'm planning to separate them to analyse them separately, but I don't know how?
Sir, here after see the tutorial of homology modelling via modeller, but I have faced problem which is shown in the pic., i.e."Volume in drive C has no label " and may be for that the model structures will not generate. So, sir, how can I fix this, please help me. (I've already posted this same query in your fb page with photo) Thanks
I understand that sometimes there might be unexpected loop regions because the sequence might not have template amino acids to align to, in that case, is it okay to leave the template as is? or would you add another template so to ensure your entire sequence is covered? Lastly, if there arent any proteins aligning to that part of your protein sequence, is it okay to leave it as a loop? your expertise would be greatly appreciated. thank you
Thanks for watching.. 1. In Homology modeling, using multiple templates always gives u a best results, if any templates matches with ur target sequence u defi. need to consider. 2. if ur loop region not falls under domain or structural motif region, u can trim that region. But, If u want to do further structural analysis, In my opinion its better to go with full length model, (use loop optimization or ab-initio modeling -to build the loop), Even-though, we are not sure the structural confirmation accurate or not in biologically. But it always give u chance to look insight of the full length model.
Hello Sir, your previous videos were also very helpful for me to do docking, but in this part I am facing some problems, How shall I rectify them ???? As I performed the exact steps shown in both video. It would be grateful sir if you can help. 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-multiple.py", line 21, in ? a.make() # do the actual comparative modeling File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 141, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 612, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 573, in read_alignment aln.append(file=self.alnfile, align_codes=codes) File "C:\Program Files\Modeller10.1\modlib\modeller\alignment.py", line 82, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 2y3a IT WILL BE GRATEFUL IF SIR YOU CAN HELP WITH THIS !!!!
Your welcome... For X-ray = structureX’ For NMR = ’structureN’ For model = ’structureM’ For Electron Microscopy = ’structureE’ For fiber diffraction = ’structureF’ For neutron diffraction = ’structureU’
I got one error while modelling post fusion spike protein saying sequence difference between alignment and pdb . I removed missing residues in templates as you suggested .How can i resolve the issue?
Sir, thanks for your detailed information. This video is much helpful. But problem is, the command line of modeller software I give you what you input into this tutorial. but software says," the system cannot find the path specified" when I command,"C:\Users>cd 2DAD". What can I do for that? Sir,if you please describe the command line what after what is input in command line, it will be helpful. Thank you!
Thanks for ur message... the command, I used in the modeller program is for my PC desktop path.. u have to use ur PC path .. u can check your path like this.. -- Check this link imgur.com/a/79A0MlL
Thank you sir for your helpful reply. But sorry to say, I can't understand how to write this command, thus I can't run modeller software for proper command line like you. Sir,can I get your mail id,please?
I-Tasser generally used to perform ab-intio modeling. Where as, the Swissmodel and Modeller are homology modeling tools, but they use different algorithm and principle to build protein 3D model. Swissmodel server uses the rigid-body assembly methods, where a model is assembled from a small number of rigid bodies obtained from the core of the aligned regions . The assembly involves fitting the rigid bodies onto the framework and rebuilding the non conserved parts, i.e., loops and side chains. Where as the modeller performs modeling by satisfaction of spatial restraints” use a set of restraints derived from the alignment, and the model is then obtained by minimizing the violations to these restraints.
Respected Sir, It's a blessing to learning from you something. Sir, I am regularly following your video and really honored to able to connect with you with this channel. Sir, I am working on a protein and I want to discuss with you regarding that; if possible can you please gave me your email id so that I can draft an email. Kind Regards, Kavita
Thanku sir for explaining in detail
Very informative
Most welcome
Im so happy I stumbled across this video, this has helped me so much, thank you.
Thanks for this effective tutorial. It’s very much elaborative to understand the overall process. I have one confusion. How will I understand which residues are missing? Would you please elaborate the process of identifying missing residues.
An excellent video. Thank you
Thank you sir for good and understandable explanation
Thank you for the great explaination.
Just one question, Can you show us sometime how to perform GROMACS MD simulaton for loop optimization ?
Thank u ... Soon we will have full session on Gromacs MD simulation Without commands
Extremely helpful tutorial 😃💖
thank you sir for this informative video!
sir very informative video.
Nicely explained.
But I want to ask what if I have selected only a single template? what command should I use? That time also I have to use model-multiple?
I followed each step carefully but still, it shows an error while running the final command.
use similar steps ... but instead of model-multiple file u have to use model-defult.py file u can get that from this folder
C:\Program Files\Modeller9.24\examples\automodel\model-default.py
Thank you so much sir..
Ur Welcome..
Sir, loop refinement is or is not mandatory? Say, I have got good folded model unlike your tutorial then could I skip loop refinement part or should I go for loop refinement?
Thank you so much for the youtube video. Please my question is I am trying to find the missing residue but it use to tell me cannot find the MISSING, What should I do?
My second question is that in my PDB Target sequence there are some missing amino acid what should I do with the gap or missing amino acid
if u having an issue with ur protein, u need to rebuild protein using any homology modeling tool, and u can use the model autodock. If u use the build protein model u can skp repair missing atom step in atudock.
Thnx for great explanation. I've a question, as you put structureX for X-ray diffraction, what letter we will put for cryo-EM experimental method?
Hello Sir, your previous videos were also very helpful for me to do docking, but in this part I am facing some problems, How shall I rectify them ???? As I performed the exact steps shown in both video. It would be grateful sir if you can help.
Sir, very good video... I have a question, How can we create a DOPE profile of the model?
sir what to do if I have no unfolded chain region? should I proceed with the final outcome structure
Great explanation, but i got error while running comand line . Actually the templates that I'm using don't have pdb format. In RCSB ,pdb format download option was not available so I downloaded the templates from pdb like zip file format. When I unzip them, there were 3 files for each protein (file name: pdb bundle 1 to pdb bundle 3 ) . I don't have any idea which pdb file for each protein is correct.
If we have the reference structure which is solved by nmr spectroscopy how we can mention in that statement like X for xray diffraction
Sir your presentation was awesome. But I have 2 questions.
1. Why dope score always negative?
2. Why lowest dope score indicates better quality of modeled protein structure?
Thanks in advance.
check this link salilab.org/modeller/tutorial/basic.html
Thanks.
Professor what if we use 2 template and secondone have 2 chains(A,B) and both the chain is involved in alignment generation by ClustalΩ so when we convert this ClustalΩ fasta alignment file into ali format so we consider the residue range till B chain endedone ? (>P1;7dwmA
structureX:7dwm.pdb:2:A:+235 here the end residue consider chain A or B)and in model_mult.py how I can put the chain B.
if we take resoultion factor and r value from crystalline structure which is already available in PDB, then why we are doing homology modeling?......model is already done.
Excellent 👌
Thanks for watching
How we know which template have more similar with target one accourding your tutorial selected protein
Some sequence are missing my homology model. For example my protein has 642 amino acid sequence but after modelling i saw 636 amino acid in pymol..I did everything accurately....i did loop optimization also...but result is same.would you like to explain it to me plesse?
How to do modelling of trimeric proteins (multichain ) as in py file for multichain modelling we can do till 2 models one. If I am editing the .py for trimeric one by including s3 , it's giving syntax error . I edited alignment file too by putting/ . What are all the methods to do multichain , multitemplate modelling ? What should we do for transmembrane region of protein ?
Good evening everyone, I need your help. I have a database of molecules in the form of an SDF file and I'm planning to separate them to analyse them separately, but I don't know how?
Sir, here after see the tutorial of homology modelling via modeller, but I have faced problem which is shown in the pic., i.e."Volume in drive C has no label " and may be for that the model structures will not generate. So, sir, how can I fix this, please help me.
(I've already posted this same query in your fb page with photo)
Thanks
is the same process will followed for loop optimization if there is error in model?
I understand that sometimes there might be unexpected loop regions because the sequence might not have template amino acids to align to, in that case, is it okay to leave the template as is? or would you add another template so to ensure your entire sequence is covered? Lastly, if there arent any proteins aligning to that part of your protein sequence, is it okay to leave it as a loop? your expertise would be greatly appreciated. thank you
Thanks for watching..
1. In Homology modeling, using multiple templates always gives u a best results, if any templates matches with ur target sequence u defi. need to consider.
2. if ur loop region not falls under domain or structural motif region, u can trim that region. But, If u want to do further structural analysis, In my opinion its better to go with full length model, (use loop optimization or ab-initio modeling -to build the loop), Even-though, we are not sure the structural confirmation accurate or not in biologically. But it always give u chance to look insight of the full length model.
@@jaannawaz2007 Thank you so so much
Hello Sir, your previous videos were also very helpful for me to do docking, but in this part I am facing some problems, How shall I rectify them ???? As I performed the exact steps shown in both video. It would be grateful sir if you can help.
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "model-multiple.py", line 21, in ?
a.make() # do the actual comparative modeling
File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 141, in make
self.homcsr(exit_stage)
File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 612, in homcsr
aln = self.read_alignment()
File "C:\Program Files\Modeller10.1\modlib\modeller\automodel\automodel.py", line 573, in read_alignment
aln.append(file=self.alnfile, align_codes=codes)
File "C:\Program Files\Modeller10.1\modlib\modeller\alignment.py", line 82, in append
allow_alternates)
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 2y3a
IT WILL BE GRATEFUL IF SIR YOU CAN HELP WITH THIS !!!!
Hey, I’m facing same issue, were you able to resolve this ? It would be really great if you can help
Sir Thank you sir . I have one question that for Xray we used structureX so what about cryoem and NMR ? What is the one letter code for them ?
Your welcome...
For X-ray = structureX’
For NMR = ’structureN’
For model = ’structureM’
For Electron Microscopy = ’structureE’
For fiber diffraction = ’structureF’
For neutron diffraction = ’structureU’
@@jaannawaz2007 thank you sir
I got one error while modelling post fusion spike protein saying sequence difference between alignment and pdb . I removed missing residues in templates as you suggested .How can i resolve the issue?
Sir, thanks for your detailed information. This video is much helpful. But problem is, the command line of modeller software I give you what you input into this tutorial. but software says," the system cannot find the path specified" when I command,"C:\Users>cd 2DAD". What can I do for that? Sir,if you please describe the command line what after what is input in command line, it will be helpful.
Thank you!
Thanks for ur message... the command, I used in the modeller program is for my PC desktop path.. u have to use ur PC path .. u can check your path like this.. -- Check this link imgur.com/a/79A0MlL
Thank you sir for your helpful reply. But sorry to say, I can't understand how to write this command, thus I can't run modeller software for proper command line like you. Sir,can I get your mail id,please?
@@joydipbarua3647 Post ur question in this Facebook page.. facebook.com/bioinfopacer/
Thank you sir. After several tries I'm able to perform it.
@@joydipbarua3647 Well done .. Please share and like our videos... we will have more videos on bioinforamtics are coming soon
What is the difference between modeling like this way and TASSER or Swiss model?
I-Tasser generally used to perform ab-intio modeling. Where as, the Swissmodel and Modeller are homology modeling tools, but they use different algorithm and principle to build protein 3D model.
Swissmodel server uses the rigid-body assembly methods, where a model is assembled from a small number of rigid bodies obtained from the core of the aligned regions . The assembly involves fitting the rigid bodies onto the framework and rebuilding the non conserved parts, i.e., loops and side chains. Where as the modeller performs modeling by satisfaction of spatial restraints” use a set of restraints derived from the alignment, and the model is then obtained by minimizing the violations to these restraints.
@@jaannawaz2007 Thank you!!
Sir, I’m not able to open pir server
18:39, what is mod9.24?
Modeller version 9.24....if you are using 9.21 version then you should use mod9.21
Respected Sir,
It's a blessing to learning from you something. Sir, I am regularly following your video and really honored to able to connect with you with this channel. Sir, I am working on a protein and I want to discuss with you regarding that; if possible can you please gave me your email id so that I can draft an email.
Kind Regards,
Kavita
Thanks a lot sir u are blessing for me very informative lecture
It's my pleasure