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Protein Structure Prediction

Volume 1137 of the series Methods in Molecular Biology pp 83-103

Date:

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

  • Daniel Barry RocheAffiliated withGenoscope, Institut de Génomique, Commissariat à l’Energie Atomique et aux Energies AlternativesCentre National de la Recherche Scientifique, UMR EvryUniversité d’Evry-Val-d’EssonnePRES UniverSud Paris, Les Algorithmes, Bâtiment Euripide
  • , Maria Teresa BuenavistaAffiliated withSchool of Biological Sciences, University of ReadingBioComputing Section, Medical Research Council Harwell, Harwell OxfordDiamond Light Source
  • , Liam James McGuffinAffiliated withSchool of Biological Sciences, University of Reading

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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.

Keywords

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