protein 3-D structure prediction

Question

[biolab]

Dear all,

I am interested in a protein of a non-model organism whose 3-D crystal structure has not been reported. However, the protein's 3-D structure of its related model species has been well studied (collected in PDB database). So I need to predict protein structure using homology approach. I used SWISS-MODEL to do this job, and found the predicted structure is quite similar with known structure. How confident this approach is? What's the popular tools for protein structure prediction? Any of your suggestions will be much appreciated.

Additionally, what tools you suggest to use for viewing protein structure (ncbi cn3d or pdbviewer or something else)? THANKS A LOT in advance!

Answer 1

[João Rodrigues]

Hi,

SWISS-MODEL is very nice, you made a good choice. Alternatives (web-based) include HHpred (which essentially links homology search with MODELLER), i-TASSER (a threading approach well-known for its accuracy) and PHYRE2 (an homology modelling server). For local purposes, MODELLER is the to-go software: it's extremely simple to install and use, the documentation and support are very good, and it's extremely versatile.

People often tend to combine the model building step with a posterior refinement step on some or all models. You can opt for a simple energy minimization protocol as those available through GROMACS or follow a more dedicated approach like for example KobaMIN (disclaimer, I built this server).

As for visualization, you can't go wrong with either PyMOL or Chimera, and I would make this your primary validation: look at the structures and see if they make sense.

[biolab]

Thank you all for your great input. I appreciate much.

Answer 2

[miquelduranfrigola]

Modeller is a quite common tool for homology modeling. Swiss-Model should be fine, also. And check ModBase or Interactome3D.

Regarding visualization, pymol is a great tool.

[biolab]

Thanks a lot for your suggestions.

Answer 3

[rjg_2186]

SWISS-MODEL should be fine, since the template structure would be close to the target protein being modeled. Modeller also gives high confidence predicted structures. You can further check the quality of the predicted protein structure using Procheck web server.