publication . Article . 2015

AnalogExplorer2 - Stereochemistry sensitive graphical analysis of large analog series.

Ye Hu; Bijun Zhang; Martin Vogt; Jürgen Bajorath;
Open Access English
  • Published: 01 Oct 2015 Journal: F1000Research (issn: 2046-1402, Copyright policy)
  • Publisher: F1000 Research Ltd
Abstract
<ns4:p>AnalogExplorer is a computational methodology for the extraction and organization of series of structural analogs from compound data sets and their graphical analysis. The method is suitable for the analysis of large analog series originating from lead optimization programs. Herein we report AnalogExplorer2 designed to explicitly take stereochemical information during graphical analysis into account and describe a freely available deposition of the original AnalogExplorer program, AnalogExplorer2, and exemplary compound sets to illustrate their use.</ns4:p>
Subjects
free text keywords: QH301-705.5, Biology (General), Bioinformatics, Macromolecular Chemistry, Medicine, R, Science, Q, Method Article, Articles, Medicinal chemistry, analog series, computational design, graphical analysis, structure-activity relationships, open access software, Biology, Data set, Open peer review, Algorithm, Neuroscience, Plant biology, Software, business.industry, business
Related Organizations

1 Agrafiotis DK Shemanarev M Connolly PJ: SAR maps: a new SAR visualization technique for medicinal chemists.J Med Chem.2007;50(24):5926–5937. 10.1021/jm070845m 17958407 [OpenAIRE] [PubMed] [DOI]

2 Kolpak J Connolly PJ Lobanov VS: Enhanced SAR maps: expanding the data rendering capabilities of a popular medicinal chemistry tool.J Chem Inf Model.2009;49(10):2221–2230. 10.1021/ci900264n 19791782 [OpenAIRE] [PubMed] [DOI]

3 Peltason L Weskamp N Teckentrup A: Exploration of structure-activity relationship determinants in analogue series.J Med Chem.2009;52(10):3212–3224. 10.1021/jm 900107b 19397320 [OpenAIRE] [PubMed] [DOI]

4 Wawer M Bajorath J: Similarity-potency trees: a method to search for SAR information in compound data sets and derive SAR rules.J Chem Inf Model.2010;50(8):1395–1409. 10.1021/ci100197b 20726598 [OpenAIRE] [PubMed] [DOI]

5 Agrafiotis DK Wiener JJ Skalkin A: Single R-Group Polymorphisms (SRPs) and R-cliffs: an intuitive framework for analyzing and visualizing activity cliffs in a single analog series.J Chem Inf Model.2011;51(5):1122–1131. 10.1021/ci200054u 21504183 [OpenAIRE] [PubMed] [DOI]

6 Wassermann AM Bajorath J: Directed R-group combinat ion graph: a methodology to uncover structure-activity relationship patterns in a series of analogues.J Med Chem.2012;55(3):1215–1226. 10.1021/jm201362h 22248436 [OpenAIRE] [PubMed] [DOI]

7 Wassermann AM Haebel P Weskamp N: SAR matrices: automated extraction of information-rich SAR tables from large compound data sets.J Chem Inf Model.2012;52(7):1769–1776. 10.1021/ci300206e 22657271 [OpenAIRE] [PubMed] [DOI]

8 Gupta-Ostermann D Bajorath J: The ‘SAR matrix’ method and its extensions for applications in medicinal chemistry and chemogenomics [v2; ref status: indexed, http://f1000r.es/3rg].F1000Res.2014;3:113. 10.12688/f1000research.4185.2 25383183 [OpenAIRE] [PubMed] [DOI]

9 Zhang B Hu Y Bajorath J: AnalogExplorer: a new method for graphical analysis of analog series and associated structure-activity relationship information.J Med Chem.2014;57(21):9184–9194. 10.1021/jm501391g 25333505 [OpenAIRE] [PubMed] [DOI]

10 Kenny PW Sadowski J: Structure Modification in Chemical Databases. In Chemoinformatics in Drug Discovery Oprea TI, (Ed.), Wiley-VCH, Weinheim, Germany,2005;271–285. 10.1002/3527603743.ch11 [OpenAIRE] [DOI]

11 Bemis GW Murcko MA: The properties of known drugs. 1. Molecular frameworks.J Med Chem.1996;39(15):2887–2893. 10.1021/jm9602928 8709122 [OpenAIRE] [PubMed] [DOI]

12 Hu Y Zhang B Vogt M: AnalogExplorer and AnalogExplorer2.ZENODO.2015 Data Source

13 Bento AP Gaulton A Hersey A: The ChEMBL bioactivity database: an update.Nucleic Acids Res.2014;42(Database issue):D1083–D1090. 10.1093/nar/gkt1031 24214965 [OpenAIRE] [PubMed] [DOI]

Abstract
<ns4:p>AnalogExplorer is a computational methodology for the extraction and organization of series of structural analogs from compound data sets and their graphical analysis. The method is suitable for the analysis of large analog series originating from lead optimization programs. Herein we report AnalogExplorer2 designed to explicitly take stereochemical information during graphical analysis into account and describe a freely available deposition of the original AnalogExplorer program, AnalogExplorer2, and exemplary compound sets to illustrate their use.</ns4:p>
Subjects
free text keywords: QH301-705.5, Biology (General), Bioinformatics, Macromolecular Chemistry, Medicine, R, Science, Q, Method Article, Articles, Medicinal chemistry, analog series, computational design, graphical analysis, structure-activity relationships, open access software, Biology, Data set, Open peer review, Algorithm, Neuroscience, Plant biology, Software, business.industry, business
Related Organizations

1 Agrafiotis DK Shemanarev M Connolly PJ: SAR maps: a new SAR visualization technique for medicinal chemists.J Med Chem.2007;50(24):5926–5937. 10.1021/jm070845m 17958407 [OpenAIRE] [PubMed] [DOI]

2 Kolpak J Connolly PJ Lobanov VS: Enhanced SAR maps: expanding the data rendering capabilities of a popular medicinal chemistry tool.J Chem Inf Model.2009;49(10):2221–2230. 10.1021/ci900264n 19791782 [OpenAIRE] [PubMed] [DOI]

3 Peltason L Weskamp N Teckentrup A: Exploration of structure-activity relationship determinants in analogue series.J Med Chem.2009;52(10):3212–3224. 10.1021/jm 900107b 19397320 [OpenAIRE] [PubMed] [DOI]

4 Wawer M Bajorath J: Similarity-potency trees: a method to search for SAR information in compound data sets and derive SAR rules.J Chem Inf Model.2010;50(8):1395–1409. 10.1021/ci100197b 20726598 [OpenAIRE] [PubMed] [DOI]

5 Agrafiotis DK Wiener JJ Skalkin A: Single R-Group Polymorphisms (SRPs) and R-cliffs: an intuitive framework for analyzing and visualizing activity cliffs in a single analog series.J Chem Inf Model.2011;51(5):1122–1131. 10.1021/ci200054u 21504183 [OpenAIRE] [PubMed] [DOI]

6 Wassermann AM Bajorath J: Directed R-group combinat ion graph: a methodology to uncover structure-activity relationship patterns in a series of analogues.J Med Chem.2012;55(3):1215–1226. 10.1021/jm201362h 22248436 [OpenAIRE] [PubMed] [DOI]

7 Wassermann AM Haebel P Weskamp N: SAR matrices: automated extraction of information-rich SAR tables from large compound data sets.J Chem Inf Model.2012;52(7):1769–1776. 10.1021/ci300206e 22657271 [OpenAIRE] [PubMed] [DOI]

8 Gupta-Ostermann D Bajorath J: The ‘SAR matrix’ method and its extensions for applications in medicinal chemistry and chemogenomics [v2; ref status: indexed, http://f1000r.es/3rg].F1000Res.2014;3:113. 10.12688/f1000research.4185.2 25383183 [OpenAIRE] [PubMed] [DOI]

9 Zhang B Hu Y Bajorath J: AnalogExplorer: a new method for graphical analysis of analog series and associated structure-activity relationship information.J Med Chem.2014;57(21):9184–9194. 10.1021/jm501391g 25333505 [OpenAIRE] [PubMed] [DOI]

10 Kenny PW Sadowski J: Structure Modification in Chemical Databases. In Chemoinformatics in Drug Discovery Oprea TI, (Ed.), Wiley-VCH, Weinheim, Germany,2005;271–285. 10.1002/3527603743.ch11 [OpenAIRE] [DOI]

11 Bemis GW Murcko MA: The properties of known drugs. 1. Molecular frameworks.J Med Chem.1996;39(15):2887–2893. 10.1021/jm9602928 8709122 [OpenAIRE] [PubMed] [DOI]

12 Hu Y Zhang B Vogt M: AnalogExplorer and AnalogExplorer2.ZENODO.2015 Data Source

13 Bento AP Gaulton A Hersey A: The ChEMBL bioactivity database: an update.Nucleic Acids Res.2014;42(Database issue):D1083–D1090. 10.1093/nar/gkt1031 24214965 [OpenAIRE] [PubMed] [DOI]

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