Docking, scoring, and affinity prediction in CAPRI

By Marc F. Lensink, Shoshana J. Wodak. 2013

248 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

Score_set: A CAPRI benchmark for scoring protein complexes (2014, background): “These criteria are based on a rigorous comparison to the targets structures in each CAPRI Round as illustrated in Table I.26–28 The criteria include the quantities f nat and f non - nat , representing respectively the fraction of receptor-ligand residue contacts in the target structure that is…”
Modeling complexes of modeled proteins (2017, methodology): “10 The community-wide experiment on Critical Assessment of Predicted Inter-actions, CAPRI10,11 offers an objective comparative evaluation of the existing docking approaches.”
Application of docking methodologies to modeled proteins (2020, methodology): “Docking of a protein pair was defined as successful if at least one correct prediction (acceptable, medium of high quality according to the CAPRI criteria 40 ) was present in the top N predictions.”
Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA (2023, methodology): “3 shows the performance of this network compared to the traditional sampling-based FARFAR2 method 4 and the deep learning-based DeepFoldRNA method 15 .”
Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK. (2017, methodology): “…performance of the docking, the interface RMSD measure from the community-wide experiment CAPRI (Critical Assessment of PRedicted Interactions) [31, 32] is used as criteria, which is calculated on interface residues by superimposing the docking solutions to the crystal structure of bound complex.”
Performance and its limits in rigid body protein-protein docking (2020, unknown): “A prediction is considered of high accuracy if Fnat ≥ 0.5 and LRMSD ≤ 1.0 Å or iRMSD ≤ 1.0 Å.”
Software for molecular docking: a review (2017, background): “ICM (Fernández-Recio et al. 2002) was ranked in the 2nd to 5th positions (Kozakov et al. 2013; Lensink and Wodak 2013).”
Information-driven structural modelling of protein-protein interactions. (2015, background): “In fact, this approach—information-driven docking—has become the most reliable and successful in the docking community, as shown in the latest assessment of the community-wide docking assessment experiment (CAPRI) [4, 5].”