Molecular modeling and simulation play a central role in academic and industrial research focused on physico-chemical properties and processes. The efforts carried out in this field have crystallized in a variety of models, simulation methods, and computational techniques that are examining the relationship between the structure, dynamics and functional role of biomolecules and their interactions. In particular, there has been a huge advance in the understanding of the molecular determinants that mediate the interaction between small compounds acting as ligands and their macromolecular targets. This book provides an updated description of the advances experienced in recent years in the field of molecular modeling and simulation of biomolecular recognition, with particular emphasis towards the development of efficient strategies in structure-based drug design.
Preface; recognition of ligands by macromolecular targets; thermodynamics of ligand binding; continuum solvation in biomolecular systems; bioavailability prediction at early drug discovery stages:: in vitro assays and simple physicochemical rules; computational strategies in drug design; molecular descriptors for database mining; pharmacophore models in drug design; docking and virtual screening; binding free energy calculations and scoring in small-molecule docking; COMparative BINding Energy (COMBINE) analysis as a structure-based 3D-QSAR method; accounting for target flexibility during ligand-receptor docking; enhanced sampling methods in drug design; exploring diversity of drug target sites; expanding the target space:: druggability assessment; computational strategies and challenges for targeting protein-protein interactions with small molecules; case studies; using molecular simulations and metadynamics to predict binding free energies and kinetics; the case of COX and CDK2; Computer-assisted design of drug-like synthetic libraries; index
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