Assessing the Quality of Modelled 3D Protein Structures Using the ModFOLD Server

  • Daniel Barry Roche
  • Maria Teresa Buenavista
  • Liam James McGuffin
Part of the Methods in Molecular Biology book series (MIMB, volume 1137)


Model quality assessment programs (MQAPs) aim to assess the quality of modelled 3D protein structures. The provision of quality scores, describing both global and local (per-residue) accuracy are extremely important, as without quality scores we are unable to determine the usefulness of a 3D model for further computational and experimental wet lab studies.

Here, we briefly discuss protein tertiary structure prediction, along with the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition and their key role in driving the field of protein model quality assessment methods (MQAPs). We also briefly discuss the top MQAPs from the previous CASP competitions. Additionally, we describe our downloadable and webserver-based model quality assessment methods: ModFOLD3, ModFOLDclust, ModFOLDclustQ, ModFOLDclust2, and IntFOLD-QA. We provide a practical step-by-step guide on using our downloadable and webserver-based tools and include examples of their application for improving tertiary structure prediction, ligand binding site residue prediction, and oligomer predictions.


Model quality assessment Protein tertiary structure prediction Critical Assessment of Techniques for Protein Structure Prediction (CASP) Web servers Single-model quality assessment methods Consensus-based (clustering) model quality assessment methods Per-residue error Fold recognition Ligand binding site residue prediction Oligomer prediction 



University of Reading Faculty Studentship, MRC Harwell and the Diamond Light Source Ltd. (to. M.T.B.). This research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013) under grant agreement No. 246556 (to D.B.R.).


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Daniel Barry Roche
    • 1
    • 2
    • 3
    • 4
  • Maria Teresa Buenavista
    • 5
    • 6
    • 7
  • Liam James McGuffin
    • 5
  1. 1.Genoscope, Institut de Génomique, Commissariat à l’Energie Atomique et aux Energies AlternativesEvryFrance
  2. 2.Centre National de la Recherche Scientifique, UMR EvryEvryFrance
  3. 3.Université d’Evry-Val-d’EssonneEvryFrance
  4. 4.PRES UniverSud Paris, Les Algorithmes, Bâtiment EuripideSaint-AubinFrance
  5. 5.School of Biological Sciences, University of ReadingReadingUK
  6. 6.BioComputing Section, Medical Research Council HarwellHarwell OxfordOxfordshireUK
  7. 7.Diamond Light SourceDidcotUK

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