Docking and scoring protein complexes: CAPRI 3rd Edition

By Marc F. Lensink, Raul Mendez, Shoshana J. Wodak. 2007

350 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

DockQ: A Quality Measure for Protein-Protein Docking Models (2016, methodology): “…standard, the average iRMS for the models with Medium quality classified incorrectly as High by DockQ is 1.05Å, and High quality classified incorrectly as Medium is 0.93Å, while the cutoff in iRMS between medium and high quality is 1.0Å (Medium < 1.0Å; High (cid:1) 1.0Å) according to CAPRI [10].”
Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “…by homology modeling (Marti-Renom et al., 2000; Petrey and Honig, 2005; Schwede et al., 2003); and atomicandreducedrepresentation modelsofproteincomplexes with small ligands and other macromolecules, such as nucleic acids, can be derived with various docking methods (Lensink et al., 2007).”
A Review of Deep Learning Methods for Antibodies (2020, background): “The Critical Assessment of PRedicted Interactions (CAPRI) is an annual competition in which participants are invited to submit structural modeling predictions of protein interactions for unpublished crystal structures [50].”
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm (2010, background): “protein-protein interactions: despite significant advances, no current computational method is capable of accurately predicting the strength or geometry of specific protein-protein interactions with any generality”
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15–19 (2010, methodology): “Biological information about the binding site is valuable for improving the selection of correct modes (Targets 32, 33, 34, 37, 40, and 41), despite that some experimental information may be misleading (Targets 38 and 39).”
CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK (2011, neutral): “rigid body docking method, one of the top performing methods together with HADDOCK in the CAPRI experiment”
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment (2021, methodology): “Both values are roughly in the range observed earlier: in the CASP13-CAPRI challenge the values ranged between ~11 and 12% for models of predictors and scorers,(41) they were 16% in the CASP12-CAPRI challenges(37) and 24% in the initial CAPRI evaluation in 2010.(42) At the same time, the fraction of”