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Finding Constellations in Chemical Space Through Core Analysis

Herein we introduce the constellation plots as a general approach that merges different and complementary molecular representations to enhance the information contained in a visual representation and analysis of chemical space. The method is based on a combination of a sub-structure based representa...

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Autores principales: Naveja, J. Jesús, Medina-Franco, José L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6646408/
https://www.ncbi.nlm.nih.gov/pubmed/31380353
http://dx.doi.org/10.3389/fchem.2019.00510
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author Naveja, J. Jesús
Medina-Franco, José L.
author_facet Naveja, J. Jesús
Medina-Franco, José L.
author_sort Naveja, J. Jesús
collection PubMed
description Herein we introduce the constellation plots as a general approach that merges different and complementary molecular representations to enhance the information contained in a visual representation and analysis of chemical space. The method is based on a combination of a sub-structure based representation and classification of compounds with a “classical” coordinate-based representation of chemical space. A distinctive outcome of the method is that organizing the compounds in analog series leads to the formation of groups of molecules, aka “constellations” in chemical space. The novel approach is general and can be used to rapidly identify, for instance, insightful and “bright” Structure-Activity Relationships (StARs) in chemical space that are easy to interpret. This kind of analysis is expected to be especially useful for lead identification in large datasets of unannotated molecules, such as those obtained through high-throughput screening. We demonstrate the application of the method using two datasets of focused inhibitors designed against DNMTs and AKT1.
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spelling pubmed-66464082019-08-02 Finding Constellations in Chemical Space Through Core Analysis Naveja, J. Jesús Medina-Franco, José L. Front Chem Chemistry Herein we introduce the constellation plots as a general approach that merges different and complementary molecular representations to enhance the information contained in a visual representation and analysis of chemical space. The method is based on a combination of a sub-structure based representation and classification of compounds with a “classical” coordinate-based representation of chemical space. A distinctive outcome of the method is that organizing the compounds in analog series leads to the formation of groups of molecules, aka “constellations” in chemical space. The novel approach is general and can be used to rapidly identify, for instance, insightful and “bright” Structure-Activity Relationships (StARs) in chemical space that are easy to interpret. This kind of analysis is expected to be especially useful for lead identification in large datasets of unannotated molecules, such as those obtained through high-throughput screening. We demonstrate the application of the method using two datasets of focused inhibitors designed against DNMTs and AKT1. Frontiers Media S.A. 2019-07-16 /pmc/articles/PMC6646408/ /pubmed/31380353 http://dx.doi.org/10.3389/fchem.2019.00510 Text en Copyright © 2019 Naveja and Medina-Franco. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Chemistry
Naveja, J. Jesús
Medina-Franco, José L.
Finding Constellations in Chemical Space Through Core Analysis
title Finding Constellations in Chemical Space Through Core Analysis
title_full Finding Constellations in Chemical Space Through Core Analysis
title_fullStr Finding Constellations in Chemical Space Through Core Analysis
title_full_unstemmed Finding Constellations in Chemical Space Through Core Analysis
title_short Finding Constellations in Chemical Space Through Core Analysis
title_sort finding constellations in chemical space through core analysis
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6646408/
https://www.ncbi.nlm.nih.gov/pubmed/31380353
http://dx.doi.org/10.3389/fchem.2019.00510
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