Literature DB >> 27280890

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation.

Denis Fourches1, Eugene Muratov2, Alexander Tropsha2.   

Abstract

There is a growing public concern about the lack of reproducibility of experimental data published in peer-reviewed scientific literature. Herein, we review the most recent alerts regarding experimental data quality and discuss initiatives taken thus far to address this problem, especially in the area of chemical genomics. Going beyond just acknowledging the issue, we propose a chemical and biological data curation workflow that relies on existing cheminformatics approaches to flag, and when appropriate, correct possibly erroneous entries in large chemogenomics data sets. We posit that the adherence to the best practices for data curation is important for both experimental scientists who generate primary data and deposit them in chemical genomics databases and computational researchers who rely on these data for model development.

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Year:  2016        PMID: 27280890      PMCID: PMC5657146          DOI: 10.1021/acs.jcim.6b00129

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  37 in total

1.  Repetitive flaws.

Authors: 
Journal:  Nature       Date:  2016-01-21       Impact factor: 49.962

2.  On outliers and activity cliffs--why QSAR often disappoints.

Authors:  Gerald M Maggiora
Journal:  J Chem Inf Model       Date:  2006 Jul-Aug       Impact factor: 4.956

3.  Joining the reproducibility initiative.

Authors: 
Journal:  Nat Nanotechnol       Date:  2014-12       Impact factor: 39.213

4.  Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches.

Authors:  Denis Fourches; Eugene Muratov; Feng Ding; Nikolay V Dokholyan; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2013-07-17       Impact factor: 4.956

5.  Expanding the scope of drug repurposing in pediatrics: the Children's Pharmacy Collaborative.

Authors:  Julie Blatt; Sherif Farag; Seth J Corey; Zafeira Sarrimanolis; Eugene Muratov; Denis Fourches; Alexander Tropsha; William P Janzen
Journal:  Drug Discov Today       Date:  2014-08-19       Impact factor: 7.851

6.  Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research.

Authors:  Denis Fourches; Eugene Muratov; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2010-07-26       Impact factor: 4.956

7.  Data set modelability by QSAR.

Authors:  Alexander Golbraikh; Eugene Muratov; Denis Fourches; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2014-01-08       Impact factor: 4.956

Review 8.  Minimum information about a bioactive entity (MIABE).

Authors:  Sandra Orchard; Bissan Al-Lazikani; Steve Bryant; Dominic Clark; Elizabeth Calder; Ian Dix; Ola Engkvist; Mark Forster; Anna Gaulton; Michael Gilson; Robert Glen; Martin Grigorov; Kim Hammond-Kosack; Lee Harland; Andrew Hopkins; Christopher Larminie; Nick Lynch; Romeena K Mann; Peter Murray-Rust; Elena Lo Piparo; Christopher Southan; Christoph Steinbeck; David Wishart; Henning Hermjakob; John Overington; Janet Thornton
Journal:  Nat Rev Drug Discov       Date:  2011-08-31       Impact factor: 84.694

9.  Policy: NIH plans to enhance reproducibility.

Authors:  Francis S Collins; Lawrence A Tabak
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

10.  Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries.

Authors:  Henrike Veith; Noel Southall; Ruili Huang; Tim James; Darren Fayne; Natalia Artemenko; Min Shen; James Inglese; Christopher P Austin; David G Lloyd; Douglas S Auld
Journal:  Nat Biotechnol       Date:  2009-10-25       Impact factor: 54.908

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  67 in total

Review 1.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

2.  Chembench: A Publicly Accessible, Integrated Cheminformatics Portal.

Authors:  Stephen J Capuzzi; Ian Sang-June Kim; Wai In Lam; Thomas E Thornton; Eugene N Muratov; Diane Pozefsky; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2017-01-19       Impact factor: 4.956

3.  Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors.

Authors:  Stephen J Capuzzi; Wei Sun; Eugene N Muratov; Carles Martínez-Romero; Shihua He; Wenjun Zhu; Hao Li; Gregory Tawa; Ethan G Fisher; Miao Xu; Paul Shinn; Xiangguo Qiu; Adolfo García-Sastre; Wei Zheng; Alexander Tropsha
Journal:  J Med Chem       Date:  2018-04-17       Impact factor: 7.446

4.  Chalcones as a basis for computer-aided drug design: innovative approaches to tackle malaria.

Authors:  Marilia Nn Lima; Bruno J Neves; Gustavo C Cassiano; Marcelo N Gomes; Kaira Cp Tomaz; Leticia T Ferreira; Tatyana A Tavella; Juliana Calit; Daniel Y Bargieri; Eugene N Muratov; Fabio Tm Costa; Carolina Horta Andrade
Journal:  Future Med Chem       Date:  2019-09-26       Impact factor: 3.808

Review 5.  Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling.

Authors:  Linlin Zhao; Heather L Ciallella; Lauren M Aleksunes; Hao Zhu
Journal:  Drug Discov Today       Date:  2020-07-11       Impact factor: 7.851

6.  Exploring drug space with ChemMaps.com.

Authors:  Alexandre Borrel; Nicole C Kleinstreuer; Denis Fourches
Journal:  Bioinformatics       Date:  2018-11-01       Impact factor: 6.937

7.  Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions.

Authors:  Mary K La; Alexander Sedykh; Denis Fourches; Eugene Muratov; Alexander Tropsha
Journal:  Drug Saf       Date:  2018-11       Impact factor: 5.606

Review 8.  From flamingo dance to (desirable) drug discovery: a nature-inspired approach.

Authors:  Aminael Sánchez-Rodríguez; Yunierkis Pérez-Castillo; Stephan C Schürer; Orazio Nicolotti; Giuseppe Felice Mangiatordi; Fernanda Borges; M Natalia D S Cordeiro; Eduardo Tejera; José L Medina-Franco; Maykel Cruz-Monteagudo
Journal:  Drug Discov Today       Date:  2017-06-15       Impact factor: 7.851

9.  Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models.

Authors:  Vinicius M Alves; Alexander Golbraikh; Stephen J Capuzzi; Kammy Liu; Wai In Lam; Daniel Robert Korn; Diane Pozefsky; Carolina Horta Andrade; Eugene N Muratov; Alexander Tropsha
Journal:  J Chem Inf Model       Date:  2018-06-13       Impact factor: 4.956

10.  Computer-aided discovery of two novel chalcone-like compounds active and selective against Leishmania infantum.

Authors:  Marcelo N Gomes; Laura M Alcântara; Bruno J Neves; Cleber C Melo-Filho; Lucio H Freitas-Junior; Carolina B Moraes; Rui Ma; Scott G Franzblau; Eugene Muratov; Carolina Horta Andrade
Journal:  Bioorg Med Chem Lett       Date:  2017-04-04       Impact factor: 2.823

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