I need to do a molecular and functional characterisation of a novel antigen, in silico. Like structure, function, antigenicity and others.
Indeed homology modelling will give you the most accurate information on 3D structure, IF (and only if) you can identify a protein (template) whose structure has been solved experimentally and whose sequence is similar enough (above 30% identity) to your protein of interest. One effective method to find templates is fold recognition (threading) and there are several free web servers. I personally like Phyre: http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index
Once you find potential templates you need to align the target and template sequences. Here it is useful to incorporate additional information on secondary structure elements and patterns of conserved residues. Once you are confident you have a correct alignment, you get to the modeling step.
Good luck!
Looking for a good template for my protein has been so difficult because most of the close homologues are not annotated too.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools