They constructed a homology model of human P-gp (using the mouse P-gp as template) and successfully docked the Rhodamine B molecule, a P-gp substrate for which the experimental binding data are available.
Davies et al. 2003 [32] built homology models of DRB1*0301, DRB1*0401, and DRB1*1101 using a DRB1*0101 template structure and docked peptides into these MHC models using simulated annealing optimization with the AMBER force field in explicit water.
20 The F-spondin and unique region were modeled separately using MODELLER with 2ZOT and 3 asQ as the templates, respectively, and docked using HADDOCK.
The P. falciparum cytochrome b model was built by homology using the X-ray crystallographic coordinates for the bovine cytochrome bc1 complex co-crystallized with stigmatellin A (PDB ID 1PP9) as a template, and fully flexible ligand docking was performed with Glide (version 5.5; Schrödinger).
Two homology models of P2Y14R based on either an agonist- or antagonist-bound structure of P2Y12R were generated as templates and compared for docking performance.
Next, new compounds with good template shape matches and low receptor docking scores were selected for the next round of shape searching and docking.
As such effects are likely to impact other targets as well, the study should aid future target-based drug design efforts by highlighting important considerations beyond the selection of a receptor template for docking studies.
Curated protein structures, docking grids, complete list of Docking Scores, and docking poses for all compounds are available upon request.
To evaluate the DNA deformation upon binding to Zif268 for each DNA template, 3DNA software was used to identify helical parameters of the DNA template upon docking versus its conformational change upon stabilization due to MD simulation.
To perform molecular docking simulations we need a receptor model, a ligand, and docking software.
