Accommodating protein flexibility for structure based drug design

Efforts in storing, organizing and exploring such information have generated a growing demand for robust and sophisticated computational tools.

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The total number of protein drug targets, which included both human proteins and proteins from pathogenic organisms, was found to be 324. Around 70% of the targets belonged to 10 protein families, while almost 50% of the drugs were shown to exert their activity via 4 families: G-protein coupled receptors, nuclear receptors, ligand-gated and voltage-gated ion channels.Molecular docking, structure-based virtual screening (SBVS) and molecular dynamics (MD) are among the most frequently used SBDD strategies due to their wide range of applications in the analysis of molecular recognition events such as binding energetics, molecular interactions and induced conformational changes [6].A distinct approach in drug design comprises the use of bioactive small-molecule libraries.I also highlight approaches that combine concepts from structure- and ligand-based design.

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Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av.

Ligand-based virtual screening (LBVS), similarity searching, QSAR modeling and pharmacophore generation are some of the most useful LBDD methods [8].

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