I have been wondering what would be the current most reliable protein structure predictior from amino acid sequence. I`m interested in both ab initio and template based predictions. You may answer based on your opinion and/or provide relevant supporting data for your answer.
I recommend Rosetta (https://www.rosettacommons.org/) and/or Robetta (http://new.robetta.org/). These packages provide a variety of tools for protein structure prediction and functional design.
Dear Denis
depends a lot from your template:
1) if it has high homology with a protein with solced structure and it allign well with it then use modeller.
2) if you do not find any good template, then you need to try ab'initio methods as rosetta/robetta but this works only for small proteins.
3) in case of uncertan template, good homology but not good alligment, also i-tasser can work well.
you can find this and other information about simple bioinformatic tools for protein prediction on my blog: ProteoCool (
https://proteocool.blogspot.com)
ProteoCool°19- Simple Tools for Protein sequence analysis available at page 6)
good luck
ciao
Manuele
The material cause of the art of protein structure prediction is a collection of primary, secondary, tertiary, and quaternary structures, and relevant information about the relationships between structure, dynamics, (free) energy, function, and evolution. The efficient cause is two-fold: (i) useful software/hardware and (ii) skillful user.
I recommend Rosetta (https://www.rosettacommons.org/) and/or Robetta (http://new.robetta.org/). These packages provide a variety of tools for protein structure prediction and functional design.
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