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The ModFOLD Model Quality Assessment Server

About the latest server

The ModFOLD4 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.

Figure 1 taken from McGuffin (2008). The predicted per-residue error (left) for an example model is compared to the observed error obtained from the alignment to the native structure (right). Each image was rendered using Pymol ( The colours represent the residue accuracy according to the temperature scheme (blue indicates residues closest to the native structure; red, those furthest from the native structure).

ModFOLD server version 4.0

ModFOLD server version 3.0

ModFOLD server version 2.0

ModFOLD server version 1.1

Download standalone versions of ModFOLD, ModFOLDclust, ModFOLDclustQ and ModFOLDclust2


Please cite the following papers:

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

The server implements the IntFOLD2-TS method to generate alternative models:

Buenavista, M. T., Roche, D. B. & McGuffin, L. J. (2012) Improvement of 3D protein models using multiple templates guided by single-template model quality assessment. Bioinformatics, 28, 1851-1857. PubMed

The server implements ModFOLDclust2 to cluster models:

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

    Older papers:
    Paper describing the original ModFOLD server:
  • McGuffin, L. J. (2008) The ModFOLD Server for the Quality Assessment of Protein Structural Models. Bioinformatics, 24, 586-7. PubMed
  • CASP8 paper describing the ModFOLDclust method and ModFOLD version 2.0:
  • 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
  • Original benchmarking of the ModFOLD method:
  • McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics, 8, 345. PubMed
If you have used ModFOLDv1.1 then please also refer to the following papers which describe MODCHECK and ProQ:
  • Pettitt, C. S., McGuffin, L. J. & Jones, D. T. (2005) Improving sequenced based fold recognition by use of 3D model quality assessment. Bioinformatics, 21, 3509-3515. PubMed
  • Wallner, B. & Elofsson, A. (2003) Can correct protein models be identified? Protein Sci. 12, 1073-1086.


  • May 2013: Improved error reporting.
  • April 2013: ModFOLD4 server paper published in NAR.
  • Dec 2012: ModFOLD4 server now online and open to all users
  • Dec 2012: Success at CASP10: ModFOLD4 quasi-single model method among top ranked methods; talk given at Quality Assessment session.
  • Aug 2012: ModFOLD 4.0 open beta version online for testing please send feedback to
  • Sept 2011: ModFOLD 3.0 now includes confidence scores (p-values).
  • Oct 2010: ModFOLD version 3.0 (beta) online for testing - the method implements the multi-model methods ModFOLDclust2, ModFOLDclustQ and the single-model mode method, ModFOLD 3.0.
  • Nov 2008: ModFOLD version 2.0 online for testing - the method aims to combine the ModFOLD and ModFOLDclust methods and outputs results in QMODE2 format.
  • July 2008: Fair usage policy introduced due to high demand.
  • March 2008: The ModFOLD servlet code has been moved to a new server for CASP8.
  • Feb 2008: If models are incorrectly numbered then the server will now attempt to automatically renumber the ATOM records in each model in order to match the residue positions in the sequence.
  • Jan 2008: The ModFOLD server paper has been published in Bioinformatics.
  • Dec 2007: The DISOclust disorder prediction method has been intergrated into server. Click here for further info.
  • Oct 2007: Version 1.1 of the ModFOLD server is now online. Two programs are now available:
    1. ModFOLD v1.1 - a fast true Model Quality Assessment Program (MQAP) that works for single or multiple models.
    2. ModFOLDclust v1.1 - a slower clustering method that works for multiple models only, but also provides per-residue local quality assessement.


Tel: 0118 378 6332

Email: l.j.mcguffin

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