Assessing protein structures with a non-local atomic interaction energy.

By Francisco Melo, Ernest Feytmans. 1998

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Citations in the corpus

Toward the estimation of the absolute quality of individual protein structure models (2010, background): “…to rank alternative models of the same protein sequence (Benkert et al., 2008; Eramian et al., 2008; Marti-Renom et al., 2000; McGuffin, 2008; Melo and Feytmans, 1998; Pettitt et al., 2005; Randall and Baldi, 2008; Samudrala and Moult, 1998; Tosatto, 2005; Wallner and Elofsson, 2003; Zhou…”
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…”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “These scores include a normalized (z-score) version of DOPE as above; the GA341 score (Melo and Sali, 2007); ModPipe’s own quality score (MPQS; Pieper et al., 2011), which is a linear combination of DOPE, GA341, and other Comparative Protein Structure Modeling Using Modeller 5.6.14 Supplement 54…”
The SWISS-MODEL Repository and associated resources (2008, methodology): “The quality of the resulting model is assessed using the ANOLEA mean force potential (36).”
Distance Matrix-Based Approach to Protein Structure Prediction (2009, methodology): “General idea of our approach is based on earlier work of Sippl [48–53], Melo and Feytmans [54, 55], Garbuzynskiy [56] among others.”
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], ANOLEA [21], PROVE [22], TUNE [23], REFINER [24], and PROQRES [25].”
The SWISS-MODEL Repository: new features and functionalities (2005, methodology): “Therefore, care was taken to include only models with a high level of conﬁdence, i.e. reliable target-template alignments with a sequence identity higher than 40%, and acceptable evaluation results by Anolea (20) and Gromos (21).”
How well can the accuracy of comparative protein structure models be predicted? (2008, background): “…al. 2000; Melo et al. 2002; McGuffin and Jones 2003; Melo and Sali 2007), (2) discriminating between the native and near-native states (Sippl 1993; Melo and Feytmans 1997, 1998; Park et al. 1997; Fiser et al. 2000; Lazaridis and Karplus 2000; Zhou and Zhou 2002; Seok et al. 2003; Tsai et al.…”
Comparative protein structure modeling of genes and genomes. (2000, background): “Programs implementing this approach include VERIFY3D (105), PROSAII (169), HARMONY (184), and ANOLEA (113).”
SWISS-MODEL: an automated protein homology-modeling server (2003, background): “Optionally, WhatCheck (32) reports and evaluation by the atomic mean force potential ANOLEA (21) are provided by SWISS-MODEL to assess the quality of the model.”
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models (2004, methodology): “Protein models with a minimum length of 45 residues sharing at least 40% sequence identity with their template structure are entered into the database if their Anolea mean force potential is below 200 kJ/mol.”
Improved model quality assessment using ProQ2 (2012, unknown): “The first of them is singlemodel methods that only use information from the actual model, such as evolutionary information [8-10], residue environment compatibility [11], statistical potentials from physics [12] or knowledge-based ones [13,14], or combinations of different structural features [15-19”
Statistical potentials for fold assessment (2002, unknown): “A statistical pair potential extracted only from the sequentially nonlocal interactions in the known protein structures (Melo and Feytmans 1998), supplemented by stereochemical restraints, is optimal for describing independently from each other.”