Hi Folks! I am very new to the bioinformatics. I did a fusion protein expression in S. cerevisiae. I am interested to analyse the structure of the fusion protein with the native protein. Especially, my aim is to find about the effect of the domains in the structure of the fusion protein. I would like to know, which bioinfo application would help me in this regard.
If you have only the protein sequence, you could try to make the 3D model structure using the Protein Model Portal (http://www.proteinmodelportal.org/?pid=modelling_interactive).
With just one sequence submition you could model your protein structure in six different modeling tools simultaneously (ModWeb; M4T; SWISS-MODEL; I-TASSER; HHpred; Phyre2).
Than, you could compare the structures with pyMol software (http://www.pymol.org/).
If you have the 2 structures in PDB format, then they can be compared in the following link.
http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=pairwise
This gives u the similarity and difference between the two structures.
If you have only the protein sequence, you could try to make the 3D model structure using the Protein Model Portal (http://www.proteinmodelportal.org/?pid=modelling_interactive).
With just one sequence submition you could model your protein structure in six different modeling tools simultaneously (ModWeb; M4T; SWISS-MODEL; I-TASSER; HHpred; Phyre2).
Than, you could compare the structures with pyMol software (http://www.pymol.org/).
Thanks to your suggestions. I hope, this would help me in resolving the structure differences.
DALI (DALI Lite) is a quick and informative tool to compare known structures (but also your own, unpublished structures). It gives you scores on how similar the structures are (rmsd etc). If you want to make a structure-based sequence alignment there are plenty of softwares around these days. Best is of course to use a structural view program such as Coot if you are familiar with it. Then you can see details of the alignment. Good luck!
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