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Verify3D
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David Eisenberg's Verify3D method for the assessment of protein models with three-dimensional profiles. Reference: "Eisenberg D, Luthy R, Bowie JU. (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277:396-404."

Prosa
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Knowladge based mean fields based method. Reference: "Sippl, M.J. (1993) Recognition of Errors in Three-Dimensional Structures of Proteins. Proteins 17, 355-362."

ProQ
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ProQ and ProQres use machine-learning techniques to assign different types of quality measures to protein models (ProQ) or to parts of protein models (ProQres). Reference: "Bjorn Wallner and Arne Elofsson (2005) Identification of correct regions in protein models using structural, alignment and consensus information. Protein Sci., 15(4):900-913"

MetaMQAPII
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MetaMQAPII is a metaserver for quality assessment of protein structures optimized for theoretical models. Reference:

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