How well can the accuracy of comparative protein structure models be predicted?

By David Eramian, Narayanan Eswar, Min-Yi Shen, Andrej Sali. 2008

155 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Molecular Biology

Citations in the corpus

Toward the estimation of the absolute quality of individual protein structure models (2010, methodology): “Received on August 27, 2010; revised on November 3, 2010; accepted on November 29, 2010”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, background): “ModEval ModEval (24) reports quality scores such as predicted RMSD and native overlap, along with scores based on statistical potentials (DOPE) (25), GA341 (26) assessing the reliability of a model.”
Protein structure modeling with MODELLER. (2014, methodology): “DOPE score and the energy profile, but also the GA341 assessment score(25,26) and an estimate of the Cα RMSD and native overlap between the model and its hypothetical native structure, using the TSVMod method(27); native overlap is defined as the fraction of Cα atoms in the model that are within 3.”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “The ‘‘Fetch Scores’’ option in the results dialog was used to calculate two additional scores, Estimated C a -RMSD and Estimated Overlap relative to the hypothetical true structure (Eramian et al., 2008).”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “For each selected target–template alignment, 10 models are calculated (18), and the model with the best value of the DOPE statistical potential (25) is selected and then evaluated by several additional quality criteria: (i) target–template sequence identity, (ii) GA341 score (26), (iii) Z-DOPE score”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “They include VERIFY3D (Luthy et al., 1992), Prosa, 2003 (Sippl, 1993; Wiederstein and Sippl, 2007), HARMONY (Topham et al., 1994), ANOLEA (Melo and Feytmans, 1998), DFIRE (Zhou and Zhou, 2002), DOPE (Shen and Sali, 2006), SOAP (Dong et al., 2013), QMEAN local (Benkert et al., 2011), and TSVMod (Eram”
Comparative Protein Structure Modeling Using Modeller (2006, background): “…ModPipe’s own quality score (MPQS; Pieper et al., 2011) which is a linear combination of DOPE, GA341, and other scores, and a prediction from TSVMod (Eramian et al., 2008) of the C α root-mean-squared deviation (RMSD) and native overlap (the fraction of C α atoms within 3.5 Å of their native…”
Comparative Protein Structure Modeling Using MODELLER (2016, background): “The “Perform action on this model” menu allows for the models themselves or modeling alignments to be downloaded. scores; and a prediction from TSVMod (Eramian et al., 2008) of the Cα root-meansquared deviation (RMSD) and native overlap (the fraction of Cα atoms within 3.5 Å of their native…”