Open Access Databases and Datasets for Drug Discovery (eBook)

Antoine Daina studied Pharmacy at the University of Lausanne (Switzerland) and got a Ph.D. in Pharmaceutical Sciences from the University of Geneva. After industrial practice as computational chemist for agrochemical research and academic experience as lecturer and researcher in drug discovery, he joined the SIB Swiss Institute of Bioinformatics in 2012. He is now Senior Scientist in the Molecular Modeling Group in charge of methodological developments in the SwissDrugDesign program, of supporting drug discovery projects and of teaching computer-aided drug design. Author of 22 peer-reviewed research articles or reviews and co-inventor on 5 patents. Michael Przewosny studied chemistry at RWTH Aachen (Germany) and obtained a PhD in the field of peptides and protein chemistry at the DWI Aachen. He has over 20 years of experience in pharmaceutical research and drug discovery, having held several positions as laboratory manager in medicinal chemistry and process development. He is listed as co-inventor on 27 patents. Vincent Zoete studied Chemistry at the Ecole Nationale Supérieure de Chimie de Lille and at Lille University (France). He studied Molecular Modeling in the Karplus Lab is Strasbourg and joined the Swiss Institute of Bioinformatics (SIB) in 2004. He was Associate Group leader of the SIB Molecular Modeling Group until 2017, then Group Leader from 2017 until now. He is also an Assistant Professor in Molecular Modelling at the University of Lausanne since 2017. He is the coordinator/developer of SwissDock.ch, SwissParam.ch, SwissBioisostere.ch, SwissTargetPrediction.ch, SwissSimilarity.ch, SwissADME.ch and the author of 122 peer-reviewed research articles and reviews, and 5 patents.

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