Beware of docking!

Molecular Docking and Structure-Based Drug Design Strategies

“…MD can additionally be used to estimate the stability of a ligand-receptor complex proposed by molecular docking [101]. When a MD-generated ligand conformation deviates by more than a given RMSD value from the corresponding docking solution, the predicted ligand-receptor complex can be considered unstable [102].…”

Crystal structure, Hirshfeld analysis and molecular docking with the vascular endothelial growth factor receptor-2 of (3Z)-5-fluoro-3-(hydroxyimino)indolin-2-one

“…Before the calculations, a stereochemical evaluation of the protein structure was carried out using the Ramachandran analysis (Lovell et al, 2003) and the number of residues in favoured regions for intermolecular interactions was over 98% [see the 'Number of residues in favoured region (VEGFR-2)' in the Supporting information]. The docking simulation was performed with the GOLD 5.5 software (Chen, 2015) and a grid of 25 Å was centered on the binding site of Levatinib in the VEGFR-2 kinase (Okamoto et al, 2015). A redocking of the Levatinib compound, an oral multikinase inhibitor that selectively inhibits the vascular endothelial growth factor-2, was used as validation method for the molecular docking protocol (see the 'Re-docking of the (Fig.…”

“…The H1, H2 and H3 atoms were positioned with idealized geometry (HFIX command) and refined using a riding model, with C-H = 0.95 Å and U iso (H) = 1.2U eq (C). SHELXL2016/6 (Sheldrick, 2015b), WinGX (Farrugia, 2012); molecular graphics: DIAMOND (Brandenburg, 2006), GOLD (Chen et al, 2015), MOPAC (Stewart, 2016), CRYSTAL EXPLORER (Wolff, et al, 2012); software used to prepare material for publication: publCIF (Westrip, 2010), enCIFer (Allen et al, 2004).…”

Binary Quantitative Structure-Activity Relationship Analysis to Increase the Predictive Ability of Structure-Based Virtual Screening Campaigns Targeting Cyclooxygenase-2

“…In this article, the application of binary QSAR analysis using decision trees constructions employing PLIF bitstrings resulted from rescoring docking simulations as descriptors to increase the predictive ability of SBVS campaigns to identify potent ligands for COX-2 [27] is presented. Binary QSAR approaches, which encode the biological activities as active (1) or inactive/decoy (0) instead of using the actual values [17] were used since several comprehensive studies have reported that there was no correlation between docking scores to biological activity values [27,[32][33]. Virtual screening campaigns to distinguish between potent COX-2 ligands and their decoys [27] by employing molecular docking software PLANTS1.2 [34][35] as the backbone software followed by the PLIF identification software PyPLIF [5] for rescoring the docking results have therefore been performed.…”