Literature DB >> 34458735

De novo molecular drug design benchmarking.

Lauren L Grant1, Clarissa S Sit1.   

Abstract

De novo molecular design for drug discovery is a growing field. Deep neural networks (DNNs) are becoming more widespread in their use for machine learning models. As more DNN models are proposed for molecular design, benchmarking methods are crucial for the comparision and validation of these models. This review looks at recently proposed benchmarking methods Fréchet ChemNet Distance, GuacaMol and Molecular Sets (MOSES), and provides a commentary on their future potential applications in de novo molecular drug design and possible next steps for further validation of these benchmarking methods. This journal is © The Royal Society of Chemistry.

Entities:  

Year:  2021        PMID: 34458735      PMCID: PMC8372209          DOI: 10.1039/d1md00074h

Source DB:  PubMed          Journal:  RSC Med Chem        ISSN: 2632-8682


  31 in total

1.  Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization.

Authors:  Markus Hartenfeller; Ewgenij Proschak; Andreas Schüller; Gisbert Schneider
Journal:  Chem Biol Drug Des       Date:  2008-06-13       Impact factor: 2.817

2.  GuacaMol: Benchmarking Models for de Novo Molecular Design.

Authors:  Nathan Brown; Marco Fiscato; Marwin H S Segler; Alain C Vaucher
Journal:  J Chem Inf Model       Date:  2019-03-19       Impact factor: 4.956

3.  Fréchet ChemNet Distance: A Metric for Generative Models for Molecules in Drug Discovery.

Authors:  Kristina Preuer; Philipp Renz; Thomas Unterthiner; Sepp Hochreiter; Günter Klambauer
Journal:  J Chem Inf Model       Date:  2018-08-28       Impact factor: 4.956

4.  The Synthesizability of Molecules Proposed by Generative Models.

Authors:  Wenhao Gao; Connor W Coley
Journal:  J Chem Inf Model       Date:  2020-04-17       Impact factor: 4.956

5.  A Turing Test for Molecular Generators.

Authors:  Jacob T Bush; Peter Pogany; Stephen D Pickett; Mike Barker; Andrew Baxter; Sebastien Campos; Anthony W J Cooper; David Hirst; Graham Inglis; Alan Nadin; Vipulkumar K Patel; Darren Poole; John Pritchard; Yoshiaki Washio; Gemma White; Darren V S Green
Journal:  J Med Chem       Date:  2020-10-12       Impact factor: 7.446

6.  PubChem BioAssay: 2017 update.

Authors:  Yanli Wang; Stephen H Bryant; Tiejun Cheng; Jiyao Wang; Asta Gindulyte; Benjamin A Shoemaker; Paul A Thiessen; Siqian He; Jian Zhang
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

7.  Efficient multi-objective molecular optimization in a continuous latent space.

Authors:  Robin Winter; Floriane Montanari; Andreas Steffen; Hans Briem; Frank Noé; Djork-Arné Clevert
Journal:  Chem Sci       Date:  2019-07-08       Impact factor: 9.825

Review 8.  Advances in de Novo Drug Design: From Conventional to Machine Learning Methods.

Authors:  Varnavas D Mouchlis; Antreas Afantitis; Angela Serra; Michele Fratello; Anastasios G Papadiamantis; Vassilis Aidinis; Iseult Lynch; Dario Greco; Georgia Melagraki
Journal:  Int J Mol Sci       Date:  2021-02-07       Impact factor: 5.923

9.  ZINC: a free tool to discover chemistry for biology.

Authors:  John J Irwin; Teague Sterling; Michael M Mysinger; Erin S Bolstad; Ryan G Coleman
Journal:  J Chem Inf Model       Date:  2012-06-15       Impact factor: 4.956

Review 10.  The Different Mechanisms of Cancer Drug Resistance: A Brief Review.

Authors:  Behzad Mansoori; Ali Mohammadi; Sadaf Davudian; Solmaz Shirjang; Behzad Baradaran
Journal:  Adv Pharm Bull       Date:  2017-09-25
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