Abstract
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.
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Acknowledgments
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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Roche, D.B., Buenavista, M.T., McGuffin, L.J. (2014). Assessing the Quality of Modelled 3D Protein Structures Using the ModFOLD Server. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 1137. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0366-5_7
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