3D protein structure prediction

Question

[1961012]

which bioinformatics tools are advisable for 2D and 3D protein structure prediction?

Answer 1

[jgreener]

To add to the other answers, the best available 3D protein structure prediction method in the absence of templates is probably trRosetta, which can be run via the server or offline.

Recently (2 days ago!) the same team pre-printed RoseTTAFold, which is currently only available as a server and improves on trRosetta but doesn't reach AlphaFold2 levels.

The top secondary structure prediction methods are much of a muchness. Arguably secondary structure prediction is less important now that tertiary prediction has improved, but it still has its uses.

Answer 2

[Michael]

Google: alphafold CASP, then you will find that in fact the best software is alphafold2, but you can't have it, then alphafold1, but you can't use it (at least for new proteins), so finally it turns out the best you can actually use is i-TASSER.

Answer 3

[Mensur Dlakic]

Secondary structure prediction is a mature field where the average 3-state prediction accuracy is in the range of 80-85% for most predictors. I could give you a long list, but some of the classics are listed here.

As to 3D predictions, it depends on whether you have a template or not. For template-based predictions, especially when the template and your protein of interest share at least 40-50% identical residues, there are many servers that will do the job. Here are some I have used:

• https://modbase.compbio.ucsf.edu/modweb/
• https://swissmodel.expasy.org/
• http://www.sbg.bio.ic.ac.uk/phyre2/index.cgi

When a good template is lacking, here are some potential solutions in addition to what has already been mentioned:

• https://yanglab.nankai.edu.cn/trRosetta/
• http://raptorx.uchicago.edu/
• http://bioinf.cs.ucl.ac.uk/psipred/ (select structural contact prediction)