New Developments in Medicinal Chemistry

Volume: 2

Indexed in: EMBASE, EBSCO.

This e-book series is recommended for readers who are interested in or work with current theoretical and experimental research in medicinal chemistry, with an emphasis on computer aided-drug design ...
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Current State-of-the-art for Virtual Screening and Docking Methods

Pp. 3-169 (167)

Carlton Anthony Taft and Carlos Henrique Tomich de Paula da Silva

Abstract

The current state of the art for docking and virtual screening methods in drug design have been reviewed, emphasizing their important contribution in aiding drug design and discovery. We summarize our contributions during the last decade, with proposals of novel inhibitors for Cancer, AIDS, Diabetes, Parkinson, Alzheimer and other diseases. Homology, fragment, consensus, bioisosteric, scaffold, pharmacophore, induced fit, chemogenomics and knowledge-based protocols have been described. The basics have been given for binding affinities, molecular dynamics, water and solvation, QM, QM/MM, free energy simulations, molecular shapes and fields. We also discuss virtual screening and comment on hotspots (protein docking, stem cells, workflow pipelines, different types of ligands/targets, cloud, high-performance, grid computing, chemical libraries, evaluations, benchmarks and validations). We describe the procedures of fifty programs that use the protocols reviewed.

Keywords:

Binding affinity, biosiosteric, chemical libraries, chemogenomics, confidence, consensus, evaluations benchmarks, fragment, future trends, homology, induced fit, knowledge based, pharmacophore, recent virtual screening and docking programs, scaffold, similarity, validations.

Affiliation:

Brazilian Center for Physics Research, Rua Dr. Xavier Sigaud, 150, Urca, 22290-180, Rio de Janeiro, Brazil.