Topology prediction is a bioinformatics tool which assist in mapping the surface of the functional protein. Which software imparts the best topology prediction?
Use as many as you can and compare the results. Do not believe any single piece of software. Check the predictions with known biochemical data to see if they agree. Be aware that topology prediction is not about mapping the surface but (for a helical membrane protein) predicting the orientation of helices in the membrane, and therefore the location of intervening loops, whether on the outside, or inside.
I have same issue for point mutation in coding region. I check the effect of AA changes by MuPRO and SIFT. I used Phyre 2, PSIPRED, SWISS-MODEL, HHCCEE, for prediction of 2d and 3d structure but I don't know how to interpret the result. If anybody help I appreciate.
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