Open Access Databases and Datasets for Drug Discovery

by Daina, Antoine; Przewosny, Michael T; Zoete, Vincent; Mannhold, Raimund; Buschmann, Helmut; Holenz, Jö; rg

• ISBN13: 9783527348398
• ISBN10: 3527348395
• Edition: 1st
• Format: Hardcover
• Copyright: 2024-02-05
• Publisher: Wiley-VCH

Summary

Comprehensive resource discussing the future of data-driven drug discovery and the growing number of open-source databases

With an overview of 90 freely accessible databases and datasets on all aspects of drug design, development, and discovery, Open Access Databases and Datasets for Drug Discovery is a comprehensive guide to the vast amount of "free data" available to today's pharmaceutical researchers. Throughout the text, the applicability of open-source data for drug discovery and development is analyzed, and their usefulness in comparison with commercially available tools is evaluated.

The most relevant databases for small molecules, drugs and druglike substances, ligand design, protein 3D structures (both experimental and calculated), and human drug targets are described in depth, including practical examples of how to access and work with the data. The first part is focused on databases for small molecules, followed by databases for macromolecular targets and diseases. The final part shows how to integrate various open-source tools into the academic and industrial drug discovery and development process.

Contributed to and edited by experts with long-time experience in the field, Open Access Databases and Datasets for Drug Discovery includes information on:

• A comprehensive listing of open access databases and datasets for computer-aided drug design
• PubChem as a chemical database for drug discovery, DrugBank Online, and bioisosteric replacement for drug discovery supported by the SwissBioisostere database
• The Protein Data Bank (PDB) and macromolecular structure data supporting computer-aided drug design, and the SWISS-MODEL repository of 3D protein structures and models
• PDB-REDO in computational aided drug design (CADD), and mining for bioactive molecules in databases

Unmatched in scope and comprehensively reviewing small and large open data sources relevant for rational drug design, Open Access Databases and Datasets for Drug Discovery is an essential reference for medicinal and pharmaceutical chemists, and any scientists involved in the drug discovery and drug development.

Author Biography

Antoine Daina is Senior Scientist at the Swiss Institute of Bioinformatics (SIB) in charge of methodological developments in the SwissDrugDesign program. Michael Przewosny has over 20 years of experience in pharmaceutical research and drug discovery, having worked as laboratory manager for different pharmaceutical companies. Vincent Zoete is a Group Leader at the Swiss Institute of Bioinformatics (SIB) and an Assistant Professor in Molecular Modelling at the University of Lausanne.

Table of Contents

INTRODUCTION

Open access databases and datasets for computer-aided drug design: A short list used in the Molecular Modelling Group of the SIB

PART 1: SMALL MOLECULES

PubChem: A Large-Scale Public Chemical Database for Drug Discovery

DrugBank Online: A How-to Guide

Bioisosteric replacement for drug discovery supported by the SwissBioisostere database

PART 2: MOLECULAR TARGETS

The Protein Data Bank (PDB) and macromolecular structure data supporting computer-aided drug design

The SWISS-MODEL repository of 3D protein structures and models

PDB-REDO in computational aided drug design (CADD)

Pharos & TRCD: Informatics tools for illuminating dark targets

PART 3: USER'S POINTS OF VIEW

Mining for bioactive molecules in open databases

Open access databases - an industrial view