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Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis

Key-based substructural fingerprints are an important element of computer-aided drug design techniques. The usefulness of the fingerprints in filtering compound databases is invaluable, as they allow for the quick rejection of molecules with a low probability of being active. However, this method is...

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Autores principales: Rataj, Krzysztof, Czarnecki, Wojciech, Podlewska, Sabina, Pocha, Agnieszka, Bojarski, Andrzej J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100401/
https://www.ncbi.nlm.nih.gov/pubmed/29789513
http://dx.doi.org/10.3390/molecules23061242
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author Rataj, Krzysztof
Czarnecki, Wojciech
Podlewska, Sabina
Pocha, Agnieszka
Bojarski, Andrzej J.
author_facet Rataj, Krzysztof
Czarnecki, Wojciech
Podlewska, Sabina
Pocha, Agnieszka
Bojarski, Andrzej J.
author_sort Rataj, Krzysztof
collection PubMed
description Key-based substructural fingerprints are an important element of computer-aided drug design techniques. The usefulness of the fingerprints in filtering compound databases is invaluable, as they allow for the quick rejection of molecules with a low probability of being active. However, this method is flawed, as it does not consider the connections between substructures. After changing the connections between particular chemical moieties, the fingerprint representation of the compound remains the same, which leads to difficulties in distinguishing between active and inactive compounds. In this study, we present a new method of compound representation—substructural connectivity fingerprints (SCFP), providing information not only about the presence of particular substructures in the molecule but also additional data on substructure connections. Such representation was analyzed by the recently developed methodology—extreme entropy machines (EEM). The SCFP can be a valuable addition to virtual screening tools, as it represents compound structure with greater detail and more specificity, allowing for more accurate classification.
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spelling pubmed-61004012018-11-13 Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis Rataj, Krzysztof Czarnecki, Wojciech Podlewska, Sabina Pocha, Agnieszka Bojarski, Andrzej J. Molecules Article Key-based substructural fingerprints are an important element of computer-aided drug design techniques. The usefulness of the fingerprints in filtering compound databases is invaluable, as they allow for the quick rejection of molecules with a low probability of being active. However, this method is flawed, as it does not consider the connections between substructures. After changing the connections between particular chemical moieties, the fingerprint representation of the compound remains the same, which leads to difficulties in distinguishing between active and inactive compounds. In this study, we present a new method of compound representation—substructural connectivity fingerprints (SCFP), providing information not only about the presence of particular substructures in the molecule but also additional data on substructure connections. Such representation was analyzed by the recently developed methodology—extreme entropy machines (EEM). The SCFP can be a valuable addition to virtual screening tools, as it represents compound structure with greater detail and more specificity, allowing for more accurate classification. MDPI 2018-05-23 /pmc/articles/PMC6100401/ /pubmed/29789513 http://dx.doi.org/10.3390/molecules23061242 Text en © 2018 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Rataj, Krzysztof
Czarnecki, Wojciech
Podlewska, Sabina
Pocha, Agnieszka
Bojarski, Andrzej J.
Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title_full Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title_fullStr Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title_full_unstemmed Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title_short Substructural Connectivity Fingerprint and Extreme Entropy Machines—A New Method of Compound Representation and Analysis
title_sort substructural connectivity fingerprint and extreme entropy machines—a new method of compound representation and analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100401/
https://www.ncbi.nlm.nih.gov/pubmed/29789513
http://dx.doi.org/10.3390/molecules23061242
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