Hi
Predicting 3D structure of novel synthesized peptides and proteins is an important step in designing new proteins like enzymes and receptors.
Can anyone suggest protein 3D structure prediction software that is user-friendly and suitable for amateur users; at the same time it ensures acceptable level of reliability and accuracy.
Sincerely.
Moein.
When designing fusion proteins, you usually want to preserve the structure of the individual domains. You therefore, whenever possible, start from the structures or good models of the individual domains, move these into the desired relative orientation using a graphical modelling tool, e.g. DeepView, Chimera or even just PyMOL, then decide on the optimal linker. For flexible linkers, I prefer Gly/Ser linkers. As a rule of thumb, I use about half as many amino acids as the distance in Å (this would be sufficient to bridge the distance of the ends to be connected in a semicircle, assuming a beta-sheet conformation). For a rigid linker based on a continuous helix, I start from an ideal alpha helix and superimpose the two domains onto this helix in different rasters, select those that do not lead to clashes to get models with different relative orientation, then optimise the sequence of the linker region using rosetta fixBB.
for more information, see
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In other cases, the linkage may be flexible, but a minimal length of the linker is crucial:
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Mohammad Moein Sadeghi
The Swiss model server predicts the 3D structure of a protein from sequence information
Mohammad Moein Sadeghi
The accuracy of the structure prediction depending on the level of sequence similarity between target and template sequences.
Seyyed Mohammad Amin Kashani
Thanks for your helpful comment.
I think your suggestions are useful in docking.
s. Thamotharan
Thanks for your constructive replying.
It helped me.
Dear Mohammad Moein Sadeghi ,
It depends (of course) a bit on what you do know about your peptides and proteins.
As a starting point you can consider I-Tasser which is one of the best performing 3D prediction programs available. Just use the so-called FASTA form for every mutation you want to check.
https://zhanglab.ccmb.med.umich.edu/I-TASSER/
Again depending on what you (already) know about your peptide/protein you can obtain additional info using Heliquest to investigate matters like overall hydrophobicity, hydrophobic moment and net charge of particular regions:
http://heliquest.ipmc.cnrs.fr/
In addition you could check/verify the 3D prediction by using one of the many secondary structure prediction programs. Such like SOPMA (but there are many more!):
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html
Best regards and good luck.
PS. If you want a quick look at how to use I-Tasser, Heliquest and secondary prediction programs you can see for example:
Article The role and significance of potential lipid-binding regions...
Dear Rob Keller
Sincerely thanks for your exhaustive guidance. I will follow your explanations.
Actually I'm looking for possible 3D structure of a new fusion protein that is formed by linking some functional domains. At first preserving secondary structures of that domains in new fusion protein and then possible ultimate 3D structure of the protein is important to me.
Respectfully
When designing fusion proteins, you usually want to preserve the structure of the individual domains. You therefore, whenever possible, start from the structures or good models of the individual domains, move these into the desired relative orientation using a graphical modelling tool, e.g. DeepView, Chimera or even just PyMOL, then decide on the optimal linker. For flexible linkers, I prefer Gly/Ser linkers. As a rule of thumb, I use about half as many amino acids as the distance in Å (this would be sufficient to bridge the distance of the ends to be connected in a semicircle, assuming a beta-sheet conformation). For a rigid linker based on a continuous helix, I start from an ideal alpha helix and superimpose the two domains onto this helix in different rasters, select those that do not lead to clashes to get models with different relative orientation, then optimise the sequence of the linker region using rosetta fixBB.
for more information, see
Article DARPin-Based Crystallization Chaperones Exploit Molecular Ge...
Article Rigidly connected multispecific artificial binders with adju...
Article Structural Basis for the Selective Inhibition of c-Jun N-Ter...
Article Rigid fusions of designed helical repeat binding proteins ef...
In other cases, the linkage may be flexible, but a minimal length of the linker is crucial:
Article Development of a generic adenovirus delivery system based on...
Article Structural Basis for Eliciting a Cytotoxic Effect in HER2-Ov...
Dear Annemarie Honegger
Thank you for sharing your wisdom with me.
I wholeheartedly appreciate time you spent to reply my question.
Gratefully
Hi
I used combination of software for protein structure prediction and helped me a lot. You can use phyre 2 which will provide you maximum of the information by comparing with the online database. Later you can import the protein structure in Schroedinger software for detail analysis and comparing two protein structures.
Thank You
Hello Mohammad Moein Sadeghi
As many others have recorded their responses, supporting the usage of Phyre2 & iTASSER for designing new proteins like enzymes and receptors as you have asked, i would also suggest you the same. In addition, i would also like to add another tool to this lineup, trRosetta, a server that models your proteins based on CASP13 structure prediction. Besides, the 3D models from this server do come energy-minimized and refined by default.
The link for the server is given below:
https://yanglab.nankai.edu.cn/trRosetta/
Hope it helps.
Dear Johnson Samuel
Thanks for your helpful recommendation.
Regards.
Hi Mohammad Moein Sadeghi ,
Swiss model is quite straightforward and simple to use online tool. it uses homology modeling technique to model your 3D protein structure. Chimera modeler is another one stand alone tool you can use to model 3D structure of protein, this tool is widely used and highly confident.
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