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