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Sampling and Mapping Chemical Space with Extended Similarity Indices

Visualization of the chemical space is useful in many aspects of chemistry, including compound library design, diversity analysis, and exploring structure–property relationships, to name a few. Examples of notable research areas where the visualization of chemical space has strong applications are d...

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Detalles Bibliográficos
Autores principales: López-Pérez, Kenneth, López-López, Edgar, Medina-Franco, José L., Miranda-Quintana, Ramón Alain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10489020/
https://www.ncbi.nlm.nih.gov/pubmed/37687162
http://dx.doi.org/10.3390/molecules28176333
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author López-Pérez, Kenneth
López-López, Edgar
Medina-Franco, José L.
Miranda-Quintana, Ramón Alain
author_facet López-Pérez, Kenneth
López-López, Edgar
Medina-Franco, José L.
Miranda-Quintana, Ramón Alain
author_sort López-Pérez, Kenneth
collection PubMed
description Visualization of the chemical space is useful in many aspects of chemistry, including compound library design, diversity analysis, and exploring structure–property relationships, to name a few. Examples of notable research areas where the visualization of chemical space has strong applications are drug discovery and natural product research. However, the sheer volume of even comparatively small sub-sections of chemical space implies that we need to use approximations at the time of navigating through chemical space. ChemMaps is a visualization methodology that approximates the distribution of compounds in large datasets based on the selection of satellite compounds that yield a similar mapping of the whole dataset when principal component analysis on a similarity matrix is performed. Here, we show how the recently proposed extended similarity indices can help find regions that are relevant to sample satellites and reduce the amount of high-dimensional data needed to describe a library’s chemical space.
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spelling pubmed-104890202023-09-09 Sampling and Mapping Chemical Space with Extended Similarity Indices López-Pérez, Kenneth López-López, Edgar Medina-Franco, José L. Miranda-Quintana, Ramón Alain Molecules Article Visualization of the chemical space is useful in many aspects of chemistry, including compound library design, diversity analysis, and exploring structure–property relationships, to name a few. Examples of notable research areas where the visualization of chemical space has strong applications are drug discovery and natural product research. However, the sheer volume of even comparatively small sub-sections of chemical space implies that we need to use approximations at the time of navigating through chemical space. ChemMaps is a visualization methodology that approximates the distribution of compounds in large datasets based on the selection of satellite compounds that yield a similar mapping of the whole dataset when principal component analysis on a similarity matrix is performed. Here, we show how the recently proposed extended similarity indices can help find regions that are relevant to sample satellites and reduce the amount of high-dimensional data needed to describe a library’s chemical space. MDPI 2023-08-30 /pmc/articles/PMC10489020/ /pubmed/37687162 http://dx.doi.org/10.3390/molecules28176333 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
López-Pérez, Kenneth
López-López, Edgar
Medina-Franco, José L.
Miranda-Quintana, Ramón Alain
Sampling and Mapping Chemical Space with Extended Similarity Indices
title Sampling and Mapping Chemical Space with Extended Similarity Indices
title_full Sampling and Mapping Chemical Space with Extended Similarity Indices
title_fullStr Sampling and Mapping Chemical Space with Extended Similarity Indices
title_full_unstemmed Sampling and Mapping Chemical Space with Extended Similarity Indices
title_short Sampling and Mapping Chemical Space with Extended Similarity Indices
title_sort sampling and mapping chemical space with extended similarity indices
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10489020/
https://www.ncbi.nlm.nih.gov/pubmed/37687162
http://dx.doi.org/10.3390/molecules28176333
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