The ModFOLD4 server for the quality assessment of 3D protein models

By Liam J. McGuffin, Maria T. Buenavista, Daniel B. Roche. 2013

120 citations recorded by the source corpus.

Once you have generated a 3D model of a protein, how do you know whether it bears any resemblance to the actual structure? To determine the usefulness of 3D models of proteins, they must be assessed in terms of their quality by methods that predict their similarity to the native structure. The ModFOLD4 server is the latest version of our leading independent server for the estimation of both the global and local (per-residue) quality of 3D protein models. The server produces both machine readable and graphical output, providing users with intuitive visual reports on the quality of predicted protein tertiary structures. The ModFOLD4 server is freely available to all at: http://www.reading.ac.uk/bioinf/ModFOLD/.

Subfields: Biomedical Engineering, Materials Chemistry, Molecular Biology

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Citations in the corpus

Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO) (2019, neutral): “Within the top performing regime of this performance domain “ QMEANDisCo3 ” , 27 “ QMEANDisCo2, ” 29 “ ModFOLD6, ” 30 and “ ModFOLD7-lDDT ” 22 are clearly in the lead (Figure 3C), followed by “ QMEAN3, ” “ ModFOLD4, ” 31 and “ VoroMQA.”
Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, background): “Predictions that did not obey this latter relationship were of lower completeness; e.g., side chains or whole loops were missing.”
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models (2017, unknown): “The method has since undergone a number of updates: ModFOLD4 (17), which makes use of IntFOLD2-TS (20)models, andModFOLD5, whichmakes use of IntFOLD3-TS (21) models.”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “…for the same protein by different independent methods are available, consensus approaches have proven powerful to identify reliable areas in models and to identify segments with likely deviations from the actual structure (Ginalski et al., 2003; Kryshtafovych et al., 2013; McGuffin et al., 2013).”
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system (2015, methodology): “The 3D 347 models were quality checked using the ModFOLD4 protocol (26).”
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates (2017, methodology): “While quality assessment (QA) methods, such as ModFOLD (3), can accurately identify the magnitude of errors in models and locate where those errors are, refinement methods aim to fix the errors in models.”
Methods for estimation of model accuracy in CASP12 (2017, methodology): “1 | ModFOLD6 The ModFOLD6 server(16) is the latest version of our freely available public resource for the accuracy estimation of 3D models of proteins.(15,38,39) The ModFOLD6 server combines a pure-single and quasisingle model strategy for improving accuracy of local and global model accuracy estim”
ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction (2015, background): “Methods ∆d PCC AUC Nm Reference ResQ DAVIS-QAconsensus ModFOLD5 ModFOLD5_single ModFOLDclust2 Pcons-net Wallner Wang_deep_2 Wang_deep_3 Wang_deep_1 6.832 (0.137) 7.107 (0.170) 7.928 (0.139) 7.929 (0.139) 8.312 (0.166) 8.773 (0.202) 9.118 (0.196) 9.345 (0.236) 9.632 (0.237) 9.694 (0.240) 0.611 0.621 ”
Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12 (2018, methodology): “Important to note that historically well-performing tools such as Verify3D[33], Prosa[29] and Dfire[31] today are clearly outperformed by newer methods such as ModFOLD4[32, 50], ModFOLD6[51], VoroMQA[52], QMEANDisCo and ProQ2[32].”
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences (2015, methodology): “ModFOLD5 adopts a quasi-single model approach for quality estimation, which has been described previously (5), however with our latest approach, a greater number and variety of reference models are generated using the IntFOLD3-TS pipeline described above.”