Assessment of blind predictions of protein–protein interactions: Current status of docking methods

By Raul Mendez, Raphaël Leplae, Leonardo De Maria, Shoshana J. Wodak. 2003

436 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, methodology): “The backbone atoms of these 'interface' residues is then superposed on their equivalents in the predicted complex (model) to compute the iRMS [9].”
Score_set: A CAPRI benchmark for scoring protein complexes (2014, neutral): “30 and 31 for details).”
FastContact: rapid estimate of contact and binding free energies (2005, neutral): “Today, nearly all docking methods use some type of scoring function to differentiate between near-native complexes and non-speciﬁc encounter complexes.”
Critical assessment of methods of protein structure prediction (CASP)‐round V (2003, methodology): “the strengths and weaknesses of current methods has already been obtained.(29)”
Protein–protein interaction and quaternary structure (2008, methodology): “Details of the methods and the results can be found in the evaluation papers (Mendez et al. 2003, 2005 ; Lensink et al. 2007), and the special issues of Proteins : Structure, Function and Bioinformatics in which they appear.”
Protein–protein interaction sites are hot spots for disease‐associated nonsynonymous SNPs (2012, background): “Residues were classed as part of the interface if one of their atoms was within 5 Å of an atom of a residue from the other protein [Mendez et al., 2003].”
Performance and its limits in rigid body protein-protein docking (2020, background): “…this limitation, CAPRI generally allowed for the submission of ten models for each target (Lensink et al., 2007; Lensink andWodak, 2010, 2013; Mendez et al., 2003, 2005), although in the more recent rounds ranking of the different groups was based on the top 5 rather than the top 10…”
Docking and scoring protein interactions: CAPRI 2009 (2010, methodology): “The reader is referred to previous CAPRI reports13,15,16 for a detailed description of these criteria and the corresponding thresholds used in classifying predictions as being of ‘‘high,’’ ‘‘medium,’’ and ‘‘acceptable’’ accuracy, denoted respectively as ‘‘***,’’ ‘‘**,’’ and ‘‘*’’ in the summary…”
CAPRI: A Critical Assessment of PRedicted Interactions (2003, methodology): “The criteria are brieﬂy described below, and we refer to the article by Mendez et al. 37 in this issue for further details.”
Dockground: A comprehensive data resource for modeling of protein complexes (2018, background): “Thus, most near-native matches, in acceptable or better category, according to the CAPRI criteria 53 (201 complexes, 50.8% of the set), were ranked outside the top 100,000 in the prediction list.”