Flexible protein-protein docking.

By Alexandre M. J. J. Bonvin. Current Opinion in Structural Biology, 2006

307 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/11737c34e832313510f4912cf4622993a78b7c80

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In Materials Chemistry

In Molecular Biology

In Radiology, Nuclear Medicine and Imaging

Citations in the corpus

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK (2011, unknown): “es in structural biology is evident [2].”
High quality binding modes in docking ligands to proteins (2008, background): “However, they are frequently found to have larger RMSD values due to (1) limited inclusion of flexibility and (2) limitations of the scoring functions, which compromise between speed and quality.”
New benchmark metrics for protein-protein docking methods (2011, background): “25 Furthermore, TF approaches require the information that two input proteins interact; that is, they are not reliable in predicting whether two proteins interact or not, largely due to the limitations of force fields used for evaluating interaction energy.”
ZRANK: Reranking protein docking predictions with an optimized energy function (2007, unknown): “Recent research in protein–protein docking includes explicitly modeling flexible protein backbones 31 ; as refinement using these meth-ods is computationally intensive and would be limited in the amount of predictions that can be accommodated, this underscores the need for retaining near-native…”
FireDock: a web server for fast interaction refinement in molecular docking (2008, background): “Then, thousands of solution candidates are reﬁned and re-scored in a reﬁnement stage (5,6).”
End-to-End Learning on 3D Protein Structure for Interface Prediction (2018, background): “Docking software currently achieves low accuracy [30]: the lack of robust interface predictors for ranking candidate complexes has been identified as one of the primary issues preventing better performance [31].”
The HADDOCK web server for data-driven biomolecular docking (2010, unknown): “The incorporation of structural flexibility into docking algorithms in order to deal with this problem remains an open challenge 2 .”
Principles of Flexible Protein-Protein Docking (2008, methodology): “12,13 These articles present a variety of docking methods that incorporate protein flexibility.”
SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models (2010, background): “Further, flexible docking creates additional danger of creating an unrealistic induced fit at a non-native docking location, resulting in a false positive prediction [41,42].”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, methodology): “While flexibility has been introduced into the study of protein folding in the context of docking [31,32], particularly for the modeling of ligand binding [33], and more recently in decoy construction for ab initio folding algorithms [34,35], it has only recently been incorporated into general-purpo”