Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

By Dariusz M Plewczynski, M. Lazniewski, R. Augustyniak, Krzysztof Ginalski. 2011

385 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking (2016, background): “As mentioned above, the affinity parameter set of AutoDock-GIST tended to cause the docking failure frequently compared with that of the pose parameter set, and the incorrect binding pose then resulted in the wrong estimation of the binding affinity [91].”
Software for molecular docking: a review (2017, methodology): “Furthermore, seven commonly used programs were evaluated on the PDBbind database with 1300 protein complexes (Plewczynski et al. 2011).”
Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology (2013, result): “65) was not as strong as observed in the previous validation, but it still presents a competitive performance compared with other methods [13].”
Key Topics in Molecular Docking for Drug Design (2019, background): “The overall size of the ligand, especially if it contains a large number of rotatable bonds impacts most docking algorithms in a negative way, both in terms of computational cost of each individual docking run and in terms of docking accuracy [46].”
Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database (2019, background): “cn) that, at that time, counted on 1300 structures [8].”
Molecular docking: a powerful approach for structure-based drug discovery. (2011, background): “Various excellent reviews on docking have been published in the past [5, 1114], and many comparison studies were conducted to evaluate the relative performance of the programs [15-18].”
Latest developments in molecular docking: 2010–2011 in review (2013, methodology): “Plewczynski et al . have concluded their docking comparison investigation [56] by stating that empirical scoring functions now appear to have reached the saturation of incremental improvement, and the future of the ﬁ eld lies in the development of conceptually new approaches.”