Question: protein 3-D structure prediction
gravatar for biolab
5.8 years ago by
biolab1.2k wrote:

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!


ADD COMMENTlink modified 5.8 years ago by João Rodrigues2.5k • written 5.8 years ago by biolab1.2k
gravatar for rjg_2186
5.8 years ago by
rjg_218650 wrote:

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.

ADD COMMENTlink written 5.8 years ago by rjg_218650
gravatar for João Rodrigues
5.8 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:


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.

ADD COMMENTlink modified 7 weeks ago by RamRS25k • written 5.8 years ago by João Rodrigues2.5k

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

ADD REPLYlink written 5.8 years ago by biolab1.2k
gravatar for miquelduranfrigola
5.8 years ago by
miquelduranfrigola760 wrote:

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.

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.8 years ago by miquelduranfrigola760

Thanks a lot for your suggestions.

ADD REPLYlink written 5.8 years ago by biolab1.2k
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