757
Views
58
CrossRef citations to date
0
Altmetric
Technology Evaluation

DataWarrior: an evaluation of the open-source drug discovery tool

ORCID Icon, ORCID Icon & ORCID Icon
Pages 335-341 | Received 13 Dec 2018, Accepted 07 Feb 2019, Published online: 26 Feb 2019

References

  • Sander T, Freyss J, von Korff M, et al. DataWarrior: an open-source program for chemistry aware data visualization and analysis. J Chem Inf Model. 2015;55:460–473.
  • Brown N, Cambruzzi J, Cox PJ, et al. Big data in drug discovery. Prog Med Chem. 2018;57:277–356.
  • González-Medina M, Naveja JJ, Sánchez N, et al. Open chemoinformatic resources to explore the structure, properties and chemical space of molecules. RSC Adv. 2017;7:54153–54163.
  • Villoutreix BO, Lagorce D, Labbé CM, et al. One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. Drug Discov Today. 2013;18:1081–1089.
  • DataWarrior: an open-source program for chemistry aware data visualization and analysis. Dimensions. Digital Science & Research Solutions Inc, 2018. Available at: https://badge.dimensions.ai/details/id/pub.1003864247 cited 2018 Dec 1
  • Saldívar-González FI, Hernández-Luis F, Lira-Rocha A, et al. Manual de Quimioinformática. 1st ed. 2017. Facultad de Química, UNAM. Available at http://www.difacquim.com
  • von Korff M, Freyss J, Sander T. Flexophore, a new versatile 3D pharmacophore descriptor that considers molecular flexibility. J Chem Inf Model. 2008;48:797–810.
  • The Apache Software Foundation. The Apache Batik Project. Accessed Jan 2019. Available from: https://xmlgraphics.apache.org/batik/. 10.Jep Java−Math Expression Parser. Accessed Jan 2019. http://sourceforge.net/projects/jep/
  • Jep Java−Math Expression Parser. cited Jan 2019. http://sourceforge.net/projects/jep/
  • Jmol: an open-source Java viewer for chemical structures in 3D. cited Jan 2019. http://jmol.sourceforge.net/
  • Lowe DM, Corbett PT, Murray-Rust P, et al. Chemical Name to Structure: OPSIN, an Open Source Solution. J Chem Inf Model. 2011;51:739–753.
  • Ekit, a free open source Java HTML editor applet and application. cited Jan 2019. http://www.hexidec.com/ekit.php
  • Sunflow: An open source rendering system for photo-realistic image synthesis. cited Jan 2019. http://sunflow.sourceforge.net/
  • Graczyk PP. Gini Coefficient: A new way to express selectivity of kinase inhibitors against a family of kinases. J Med Chem. 2007;50:5773–5779.
  • Xue L, Bajorath J. Molecular descriptors in chemoinformatics, computational combinatorial chemistry, and virtual screening. Comb Chem High Throughput Screen. 2000;3:363–372.
  • Egieyeh SA, Syce J, Malan SF, et al. Prioritization of anti-malarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs. Malar J. 2016;15:50.
  • Naveja JJ, Medina-Franco JL. Activity landscape sweeping: insights into the mechanism of inhibition and optimization of DNMT1 inhibitors. RSC Adv. 2015;5:63882–63895.
  • Prieto-Martínez FD, Gortari EF-D, Méndez-Lucio O, et al. A chemical space odyssey of inhibitors of histone deacetylases and bromodomains. RSC Adv. 2016;6:56225–56239.
  • Rocha-Roa C, Cossio-Pérez R, Molina D, et al. In silico study of Moxifloxacin derivatives with possible antibacterial activity against a resistant form of DNA gyrase from Porphyromonas gingivalis. Arch Oral Biol. 2018;95:30–39.
  • López-López E, Prieto-Martínez F, Medina-Franco J. Activity landscape and molecular modeling to explore the SAR of dual epigenetic inhibitors: A focus on G9a and DNMT1. Molecules. 2018;23:3282.
  • Lenci E, Innocenti R, Menchi G, et al. Diversity-oriented synthesis and chemoinformatic analysis of the molecular diversity of sp3-rich morpholine peptidomimetics. Front Chem. 2018;6:522.
  • Alves VM, Muratov EN, Zakharov A, et al. Chemical toxicity prediction for major classes of industrial chemicals: is it possible to develop universal models covering cosmetics, drugs, and pesticides? Food Chem. Toxicol. 2018;112:526–534.
  • TIBCO Software Inc. TIBCO Spotfire. Palo Alto, CA, USA; 1996
  • Dotmatics. Dotmatics Informatics Suite. Dotmatics; 2005
  • Addinsoft. Miner3D. Paris, France: Addinsoft; 2018
  • Tableau Software. Tableau. Tableau Software; 2018
  • González-Medina M, Medina-Franco JL. Platform for unified molecular analysis: PUMA. J Chem Inf Model. 2017;57:1735–1740.
  • González-Medina M, Méndez-Lucio O, Medina-Franco JL. Activity landscape plotter: a web-based application for the analysis of structure-activity relationships. J Chem Inf Model. 2017;57:397–402.
  • Awale M, Probst D, Reymond J-L. WebMolCS: A web-based interface for visualizing molecules in three-dimensional chemical spaces. J Chem Inf Model. 2017;57:643–649.
  • Capuzzi SJ, Kim IS-J, Lam WI, et al. Chembench: A publicly accessible, integrated cheminformatics portal. J Chem Inf Model. 2017;57:105–108.
  • Chemical Computing Group. Molecular operating environment (MOE). Montreal, QC, Canada: Chemical Computing Group; 2018.
  • Duan J, Dixon SL, Lowrie JF, et al. Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J Mol Graph Model. 2010;29:157–170.
  • Sastry M, Lowrie JF, Dixon SL, et al. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J Chem Inf Model. 2010;50:771–784.
  • Osolodkin DI, Radchenko EV, Orlov AA, et al. Progress in visual representations of chemical space. Expert Opin Drug Discov. 2015;10:959–973.
  • Naveja JJ, Oviedo-Osornio CI, Trujillo-Minero NN, et al. Chemoinformatics: a perspective from an academic setting in Latin America. Mol Divers. 2018;22:247–258.
  • Gadaleta D, Lombardo A, Toma C, et al. A new semi-automated workflow for chemical data retrieval and quality checking for modeling applications. J Cheminform. 2018;10:60.
  • Sahoo S, Adhikari C, Kuanar M, et al. A short review of the generation of molecular descriptors and their applications in quantitative structure property/activity relationships. Curr Comput-Aid Drug. 2016;12:181–205.
  • Shahraki S, Shiri F, Heidari Majd M, et al. Anti-cancer study and whey protein complexation of new lanthanum(III) complex with the aim of achieving bioactive anticancer metal-based drugs. J Biomol Struct Dyn. 2018:1–14. In press. doi: 10.1080/07391102.2018.1476266
  • Hassan M, Abbas Q, Ashraf Z, et al. Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study. Comput Biol Chem. 2017;68:131–142.
  • Yosipof A, Shimanovich K, Senderowitz H. Materials informatics: statistical modeling in material science. Mol Inform. 2016;35:568–579.
  • Senderowitz H, Tropsha A. Materials informatics. J Chem Inf Model. 2018;58:2377–2379.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.