Towards more accurate pharmacophore modeling: Multicomplex-based comprehensive pharmacophore map and most-frequent-feature pharmacophore model of CDK2

Computational investigation of interactions between human H2 receptor and its agonists

“…Pharmacophore modeling is another widely used ligand-based method for drug discovery. It can be used to discover novel ligands with diverse chemical types [17][18][19]. Many pharmacophore models have been built for GPCR ligands [20,21], but none was reported for H 2 R agonists.…”

Structure-based three-dimensional pharmacophores as an alternative to traditional methodologies

“…75 In this case, a comprehensive pharmacophore map was generated based on a collection of 124 crystal structures of the human CDK2-inhibitor complex. This ensemble of structures is expected to contain almost all the chemical features important for CDK2-inhibitor interactions.…”

Receptor Chemoprint Derived Pharmacophore Model for Development of CAIX Inhibitors

“…This pharmacophore is a true representative of CAIX active site, and chemoprint based method showed superior efficiency than earlier ligand based pharmacophore model [8,35], where quality of model affected significantly with training data set selection and conformation generation method [14,15]. Moreover, Catalyst tool includes ligand information only to define the pharmacophoric feature constraint, whereas in LigandScout, the spatial complementarities of ligands with physiochemical properties of active site residues are used to determine the pharmacophore features [36].…”

“…Pharmacophore modelling, Quantitative Structure Activity Relationship (QSAR), virtual screening, docking simulation and pharmacokinetics based analyses are used for development of new chemical entities [10,13]. However, the ligand based pharmacophore models are significantly depend on selected training set and conformation generation method [14]. This technique is more suitable, when protein structure or its complex with ligand has limited information [15].…”