On the above mentioned modelling methods, which one is suitable for protein structure prediction for protein/gene families? Suggest some highly reliable modelling methods and software used for it.
Both methods have their strengths and limitations. Homology modeling is more effective when a close homologous template is available, while protein threading can provide insights when no close homologous templates are found. Popular threading tools include I-TASSER, Phyre2, and RaptorX. For homology modeling popular tools are MODELLER, SWISS-MODEL, and Rosetta.
Homology modeling will always be over the threading approach. Just Cluster alignment using BlastP and if query coverage is more than 80 and homology more than 70 .. go for homology modeling and if it resides in the range of 30-40 go for threading.. for threading iTasser is a better option.
My verify3d fails as there were no templates
with a pass verify3d. Initially they were failing
the Verify3D score at 30%. Through energy
minimization and loop modelling i brought it up
to 76 now. However it asks for 80% to be able to
pass the 3d test.
I have done enough loop modeling, refinement,
energy minimization, it is now stagnant at 76.
Please suggest how can i increase it more?
Anyone?
Also just asking, is it like compulsory to get the verify3D pass? Do reviewers really ask for it? Please guide. Thanks much already.
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