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The ModFOLD Model Quality Assessment Server

About the latest server

The ModFOLD server provides:

  1. A single score and a p-value relating to the predicted quality of a single 3D model of a protein structure.
  2. Rankings for multiple 3D models for the same protein target according to predicted model quality.
  3. Predictions of the local quality (per-residue error) within multiple models.
  4. Interactive 3D visualisations of models coloured by residue quality.
  5. Machine-readable data downloads

This website is free and open to all users and there is no login requirement.
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Fair usage policy:

You are only permitted to have 1 job running at a time for each IP address, so please wait until your previous job completes before submitting further data. If you already have a job running then you will be notified and your uploaded data will be deleted. Once your job has completed your IP address will be unlocked and you will be able to submit new data.

ModFOLD9 server submission form

Help page

Sample output

References

  • McGuffin, L.J. and Alharbi, S.M.A. (2024) ModFOLD9: a web server for independent estimates of 3D protein model quality. Journal of Molecular Biology, 436, 168531. DOI PubMed
  • McGuffin, L.J., Aldowsari, F., Alharbi, S. and Adiyaman, R. (2021) ModFOLD8: accurate global and local quality estimates for 3D protein models. Nucleic Acids Res., 49, W425–W430. DOI PubMed
  • Maghrabi, A.H.A. & McGuffin L.J. (2017) ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins. Nucleic Acids Res., 45, W416-W421. DOI PubMed
  • McGuffin, L.J., Shuid, A.M., Kempster, R., Maghrabi, A.H.A., Nealon J.O., Salehe, B.R., Atkins, J.D. & Roche, D.B. (2017) Accurate Template Based Modelling in CASP12 using the IntFOLD4-TS, ModFOLD6 and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1, 335-344, doi: 10.1002/prot.25360. PubMed

Figure 2 taken from McGuffin et al. (2013). Graphical and interactive output from the ModFOLD4 server. Top left: main results page with table showing global scores, P-values and thumbnails of graphical output (results for a single model are shown for clarity; multiple models are shown as additional rows to the table—see the examples on the help pages). Bottom left: clicking on the thumbnail image leads to a full size view of the per-residue error plot, which may be downloaded in PostScript format. Top right: clicking on the thumbnail image leads to an interactive view of model, which can be manipulated in 3D using the Jmol plug-in (http://jmol.sourceforge.net/). Bottom right: PDB files of the model can be downloaded with local quality scores added to B-factor column. The model can be viewed and rendered in PyMol (http://www.pymol.org/) using the temperature colouring option, where blues and greens represent residues predicted to be close to the native structure, whereas oranges and reds represent those that deviate from the native structure.

Papers describing older versions of ModFOLD

  • McGuffin, L.J., Buenavista, M.T., & Roche, D.B. (2013) The ModFOLD4 Server for the Quality Assessment of 3D Protein Models. Nucleic Acids Res., 41, W368-72. PubMed
  • McGuffin, L. J. & Roche, D. B. (2010) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, 26, 182-188. PubMed
  • McGuffin, L. J. (2009) Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins: Structure Function and Bioinformatics, 77, 185-190. PubMed
  • McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-7. PubMed
  • McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics, 8, 345. PubMed

Previous ModFOLD versions:

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