Docking combination

Lill MA, Dobler M, Vedani A. Prediction of small-molecule binding to cytochrome P450 3A4 Flexible docking combined with multidimensional QSAR. ChemMedChem 2006 6 73-81. 

Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 2000 43 4759-67. 

The adsorption of the modifier-substrate complex onto Pt (111) surface was investigated using the Soiids-Docking module of the Insightll package. This module determines the conformations of the adsorbed molecules by a combined approach of high temperature molecular dynanuc simulations with molecular mechanics minimization. All the calculated structures were visualized on a Silicon Graphics workstation. 

In this section, a number of case studies (Table 5) in which different types of VS methods are combined into a hybrid workflow. Often these combine a fast, ligand or pharmacophore-based method with a later docking method. The latter is useful at the inspection stage as it allows the molecule to be reviewed within the context of the protein binding site. A poor binding pose can be an indicator of a poor fit. Furthermore, possible interactions outside the scope of the molecules used to train the ligand-based method can be identified. 

Structural properties of both AFA-PLN and WT-PLN bound to SER-CAla after reconstitution in a functional lipid bilayer environment were examined by 13C solid-state NMR.241 Chemical-shift assignments in all domains of AFA-PLN provide direct evidence for the presence of two terminal ot-helices connected by a linker region of reduced structural order that differs from previous findings on free PLN. A combination of the spectroscopic data with biophysical and biochemical data using flexible protein-protein docking simulations provides a structural basis for understanding the interaction between PLN and SERCala.244 Using a... 

---