Identification of correct regions in protein models using structural, alignment, and consensus information

By Björn Wallner, Arne Elofsson. 2006

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In Molecular Biology

Citations in the corpus

Local Error Estimates Dramatically Improve the Utility of Homology Models for Solving Crystal Structures by Molecular Replacement (2015, methodology): “In general, the consensus methods have a higher accuracy, but, as shown in this study, the single-model method ProQ2 produces results similar to those of the best consensus methods (e.g., Pcomb and IntFold).”
ProQ3D: improved model quality assessments using deep learning (2016, methodology): “However, the same is observed when using Pcons, although the correlation is probably quite close to the theoretical limit, as it is higher than the correlation between different methods used to evaluate the quality of a model Wallner and Elofsson (2007).”
Prediction of global and local model quality in CASP8 using the ModFOLD server (2009, methodology): “5,15 For a residue in a pairwise superposition the S -score was defined as: where S i was the S -score for residue i in a model, d i was the distance between aligned residues according to the TM-score superposition and d 0 was the distance threshold (3.9).”
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “In order to operate, MetaMQAP combines the output from a number of model quality assessment programs (MQAPs), including VERIFY3D [18], PROSA [19], BALA-SNAPP [20], ANO-LEA [21], PROVE [22], TUNE [23], REFINER [24], and PROQRES [25].”
ProQ3: Improved model quality assessments using Rosetta energy terms (2016, background): “Availability: ProQ3 is freely available on BitBucket at https://bitbucket.org/ElofssonLab/proq3 Contact: arne@bioinfo.se”
QMEAN server for protein model quality estimation (2009, methodology): “QMEAN can also be used for assessing individual models within SWISS-MODEL Workspace (26,27) together with other tools such as ProQres (28), ANOLEA (29) and WhatCheck (30).”
Using multiple templates to improve quality of homology models in automated homology modeling (2008, methodology): “In a recent study (Wallner and Elofsson 2006), we showed that three methods, Nest (Petrey et al. 2003), Modeller (Sali and Blundell 1993), and SegMod (Levitt 1992), all perform quite well for single-template homology modeling, while several other methods frequently failed to produce…”
The SWISS-MODEL Repository and associated resources (2008, methodology): “Therefore, entries from the Repository can be directly submitted to the Workspace for quality assessment using different global and local quality scores such as DFire (45), ProQRes ( 46 ) or QMEAN (47).”
CRITICAL ASSESSMENT OF TECHNIQUES FOR PROTEIN STRUCTURE PREDICTION (2014, methodology): “For CASP12, we have implemented 6 kinds of CPIs: hydrophobic packing, confinement, secondary structure formation[6], strand pairing, hydrogen bonding, and evolutionary data[7].”
Estimation of model accuracy in CASP13 (2019, methodology): “T A B L E 1 O v e r v i e w o f m e t h o d s d i s c u ss e d i n t h i s a rt i c l e a nd t h e w a y t h e y w e r e d e v e l o p e d methods 10,11 and local accuracy assessment methods, 12 see Table 1.”
Improved model quality assessment using ProQ2 (2012, methodology): “In this study, we have used S-score as the correctness measure for each residue in a protein model.”