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FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
BACKGROUND: Drug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical c...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561050/ https://www.ncbi.nlm.nih.gov/pubmed/18816385 http://dx.doi.org/10.1186/1471-2105-9-396 |
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author | Lagorce, David Sperandio, Olivier Galons, Hervé Miteva, Maria A Villoutreix, Bruno O |
author_facet | Lagorce, David Sperandio, Olivier Galons, Hervé Miteva, Maria A Villoutreix, Bruno O |
author_sort | Lagorce, David |
collection | PubMed |
description | BACKGROUND: Drug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical compounds along the search process rather than at the final stages. Fast methods for evaluating ADMET properties of small molecules often involve applying a set of simple empirical rules (educated guesses) and as such, compound collections' property profiling can be performed in silico. Clearly, these rules cannot assess the full complexity of the human body but can provide valuable information and assist decision-making. RESULTS: This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections. FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries. CONCLUSION: We have developed FAF-Drugs2 to facilitate compound collection preparation, prior to (or after) experimental screening or virtual screening computations. Users can select to apply various filtering thresholds and add rules as needed for a given project. As it stands, FAF-Drugs2 implements numerous filtering rules (23 physicochemical rules and 204 substructure searching rules) that can be easily tuned. |
format | Text |
id | pubmed-2561050 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-25610502008-10-04 FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects Lagorce, David Sperandio, Olivier Galons, Hervé Miteva, Maria A Villoutreix, Bruno O BMC Bioinformatics Software BACKGROUND: Drug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical compounds along the search process rather than at the final stages. Fast methods for evaluating ADMET properties of small molecules often involve applying a set of simple empirical rules (educated guesses) and as such, compound collections' property profiling can be performed in silico. Clearly, these rules cannot assess the full complexity of the human body but can provide valuable information and assist decision-making. RESULTS: This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections. FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries. CONCLUSION: We have developed FAF-Drugs2 to facilitate compound collection preparation, prior to (or after) experimental screening or virtual screening computations. Users can select to apply various filtering thresholds and add rules as needed for a given project. As it stands, FAF-Drugs2 implements numerous filtering rules (23 physicochemical rules and 204 substructure searching rules) that can be easily tuned. BioMed Central 2008-09-24 /pmc/articles/PMC2561050/ /pubmed/18816385 http://dx.doi.org/10.1186/1471-2105-9-396 Text en Copyright © 2008 Lagorce et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Lagorce, David Sperandio, Olivier Galons, Hervé Miteva, Maria A Villoutreix, Bruno O FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title | FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title_full | FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title_fullStr | FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title_full_unstemmed | FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title_short | FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects |
title_sort | faf-drugs2: free adme/tox filtering tool to assist drug discovery and chemical biology projects |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2561050/ https://www.ncbi.nlm.nih.gov/pubmed/18816385 http://dx.doi.org/10.1186/1471-2105-9-396 |
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