He everyone. I have a question about protein structure prediction. When predicting the structure of a protein using various algorithms, most often I get a monomer as an output. But most often I have no idea whether the predicted protein is a dimer or a larger structure. Is there an algorithm that allows me to predict the final quaternary protein structure with any probability? Of interest are purely computer algorithms. I would be very grateful for help!
Dear Nikolai
Check out DeepComplex web server
http://tulip.rnet.missouri.edu/deepcomplex/web_index.html
Dear Nikolai Navumchyk
you can use intfold (https://www.reading.ac.uk/bioinf/IntFOLD/) or raptorX (http://raptorx.uchicago.edu/) in order to predict a protein 3D structure, you can find the list of additional tools below, such resources needs strong computational and calculation power they are mainly softwares hosted in universities servers that you can remotely use: https://molbiol-tools.ca/Protein_tertiary_structure.htm
best regards
If you are trying homology modeling, the result would depend on the structure of the template. If you take monomer of a homologous structure as template, you'll get monomer as output.
If you are getting monomer as output even after using multimeric template, you can simply superimpose several copies of the monomer on the template to generate the multimer and then do molecular dynamics simulations to check the stability.
If there is no template for higher order structure, you may need to rely on protein protein docking algorithms to predict multimers (e.g., SymmDock).
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