Hello
I'm trying to model ALSIN protein for my article. It is a quite large protein with 1657 amino acids. First, I tried to use SWISS-MODEL web server, but Based on its homolgy modeling strategy, its models can only cover half of the resides. I also tried to use I-TASSER but it cannot draw model for more than 1500 residues in every modelling process.
I wanted to know is there any other database or software to solve this problem?
Interestingly, I've found an article entitled "Alsin and the Molecular Pathways of Amyotrophic Lateral Sclerosis" which has a 3D model for this protein. But it hasn't mentioned the software or the database that this model is obtained from.
I will so pleased to receive your comments to solve this problem
Here are some suggestions:
- try to model each domain separately
- ask the corresponding author of the paper you mentioned for the model or the software they used
Hi Yousef,
I agree with Milad, since you have found the relevant paper, it is recommended that you can email the author for help. If you can’t find a better solution, I know that Creative Biostructure has the protein modeling service. This is a very professional structural biology company, maybe you can try it.
All the best!
Milad Bastami
Dear Dr. Bastami, thanks for your response. I need to add that i have a stop codon mutation in this protein and i want to compare the resulted models of normal and mutant protein in my article.
I've contacted the corresponding author of that article, but I've received no answers yet.
I thought about modelling the domains separately . Here i send the obtained functional domains from Ncbi's conserved domain database. As you can see, if i try to model them separately, it cannot cover the whole the protein.
I thought about modeling of the domain which the mutation is located . The problem is ,i have a stop codon exactly in the first amino acids of this domain, so it won't help either.
Roger Davis Thanks Dear roger
I've already contacted the corresponding author of the article. Bit still no I've got no answers. I also will contact your suggested company.
well, as there are mechanisms to compensate for the effect of some stop-codon mutation, predicting the effect of such mutation could be rather hard. I encourage you to read the following articles about rescue mechanisms of nonsense mutations:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155323/
Article Optimized approach for the identification of highly efficien...
I also found a tool for predicting the effect of nonsense mutations:
Article Ranking insertion, deletion and nonsense mutations based on ...
http://www.moseslab.csb.utoronto.ca/indelz/indelz.html
Hi dear Yousef,
after installing the I-TASSER in Linux, you can search and make your favorite model based on the protein homology; request the I-Tasser team to provide you a license to install this package in Lin. and use it. the second way, as discussed, is using the swiss-model in which you can select the different motifs/domains to integrate them is a distinct PDB file, however, I recommend the former one.
Hajira Batool Thanks. As i mentioned i tried the swiss model but but based on its homology based simulation it can't give a good model.
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