Molecular modeling protein-ligand interactions

Keywords Molecular modeling NMR spectroscopy Peptide-carbohydrate mimicry Protein-ligand interactions X-ray crystallography... 

Consider a molecular structure, which is the most important unifying information model in chemistry. Molecular structures appear in knowledgebases that represent catalogs of commercially available chemicals, pharmacology of named drugs, natural sources of bioactive molecules, protein-ligand interactions, measured molecular bioactivities, metabolic pathways, abstracted research literature, databases of synthetic reactions, and so on. 

Katchalski-Katzir, Ephraim, Molecular recognition in Biology Models for Analysis of Protein—Ligand Interactions, 1, 25. 

Molecular Recognition in Biology Models for Analysis of Protein-Ligand Interactions Lancet, Horovitz and Katchalski-Katzir) 1 25... 

Computation and Modeling of Molecular Recognition Intermolecular Interactions in Molecular Recognition Mechanisms of Enzyme Inhibition Protein-Ligand Interactions... 

Molecular modeling techniques are used extensively to supplement biophysical experimental methods for characterization of protein-ligand complexes. Modeling methods are often an essential tool for refinement of detailed structures from raw experimental data, and modeling techniques can provide additional information not readily available from experimental approaches. An overview of some modeling techniques suitable for investigation of protein-ligand interactions will be presented here. 

Cook and coworkers undertook the difficult task of correlating the data between the amino acids believed to be involved in ligand binding and the specific region of their unified pharmacophore/receptor model (90). Some of the amino acid residues likely associated with BzR ligand binding are indicated in the unified pharmacophore/receptor model presented in Fig. 14.2. There are several key protein-ligand interactions that deserve mention, but in the author s words, it is clear that "much work remains at the molecular level to determine... 

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