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Future Science OA Volume 2, 2016 - Issue 4

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Short Communication

Analog Series-Based Scaffolds: Computational Design and Exploration of a New Type of Molecular Scaffolds for Medicinal Chemistry

Dilyana Dimova1 Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113Bonn, Germany

Dagmar Stumpfe1 Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113Bonn, Germany

Ye Hu1 Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113Bonn, Germany

Jürgen Bajorath1 Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113Bonn, GermanyCorrespondence[email protected]

Article: FSO149 | Accepted 09 Sep 2016, Published online: 04 Oct 2016

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https://doi.org/10.4155/fsoa-2016-0058
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José J. Naveja, Fernanda I. Saldívar‐González, Diana L. Prado‐Romero, Angel J. Ruiz‐Moreno, Marco Velasco‐Velázquez, Ramón Alain Miranda‐Quintana & José L. Medina‐Franco. 2024. Computational Drug Discovery. Computational Drug Discovery 365 393 .

Jonas Schaub, Julian Zander, Achim Zielesny & Christoph Steinbeck. (2022) Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). Journal of Cheminformatics 14:1.
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Candida Manelfi, Marica Gemei, Carmine Talarico, Carmen Cerchia, Anna Fava, Filippo Lunghini & Andrea Rosario Beccari. (2021) “Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool. Journal of Cheminformatics 13:1.
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José J. Naveja & Martin Vogt. (2021) Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications. Molecules 26:17, pages 5291.
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J. Jesús Naveja & José L. Medina‐Franco. (2020) Consistent Cell‐selective Analog Series as Constellation Luminaries in Chemical Space. Molecular Informatics 39:12.
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Conrad V. Simoben, Ammar Qaseem, Aurélien F. A. Moumbock, Kiran K. Telukunta, Stefan Günther, Wolfgang Sippl & Fidele Ntie‐Kang. (2020) Pharmacoinformatic Investigation of Medicinal Plants from East Africa. Molecular Informatics 39:11.
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Trong D. Tran, Steven M. Ogbourne, Peter R. Brooks, Norberto Sánchez-Cruz, José L. Medina-Franco & Ronald J. Quinn. (2020) Lessons from Exploring Chemical Space and Chemical Diversity of Propolis Components. International Journal of Molecular Sciences 21:14, pages 4988.
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Atsushi Yoshimori & Jürgen Bajorath. (2020) Deep SAR matrix: SAR matrix expansion for advanced analog design using deep learning architectures. Future Drug Discovery 2:2.
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J. Jesús Naveja, B. Angélica Pilón-Jiménez, Jürgen Bajorath & José L. Medina-Franco. (2019) A general approach for retrosynthetic molecular core analysis. Journal of Cheminformatics 11:1.
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Atsushi Yoshimori, Yuichi Horita, Toru Tanoue & Jürgen Bajorath. (2019) Method for Systematic Analogue Search Using the Mega SAR Matrix Database. Journal of Chemical Information and Modeling 59:9, pages 3727-3734.
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J. Jesús Naveja & José L. Medina-Franco. (2019) Finding Constellations in Chemical Space Through Core Analysis. Frontiers in Chemistry 7.
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Elena Lenci & Andrea Trabocchi. (2019) Smart Design of Small‐Molecule Libraries: When Organic Synthesis Meets Cheminformatics. ChemBioChem 20:9, pages 1115-1123.
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Alexey A. Orlov, Vladimir P. Berishvili, Anastasia A. Nikitina, Dmitry I. Osolodkin, Eugene V. Radchenko & Vladimir A. Palyulin. 2019. In Silico Drug Design. In Silico Drug Design 359 395 .

Dimitar Yonchev, Martin Vogt, Dagmar Stumpfe, Ryo Kunimoto, Tomoyuki Miyao & Jürgen Bajorath. (2018) Computational Assessment of Chemical Saturation of Analogue Series under Varying Conditions. ACS Omega 3:11, pages 15799-15808.
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Jürgen Bajorath. (2018) Improving the utility of molecular scaffolds for medicinal and computational chemistry. Future Medicinal Chemistry 10:14, pages 1645-1648.
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Dilyana Dimova & Jürgen Bajorath. (2018) Collection of analog series-based scaffolds from public compound sources. Future Science OA 4:4, pages FSO287.
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Dilyana Dimova, Dagmar Stumpfe & Jürgen Bajorath. (2018) Computational design of new molecular scaffolds for medicinal chemistry, part II: generalization of analog series-based scaffolds. Future Science OA 4:2, pages FSO267.
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Erik Gilberg, Dagmar Stumpfe & Jürgen Bajorath. (2018) X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. ACS Omega 3:1, pages 106-111.
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Dilyana Dimova & Jürgen Bajorath. 2018. Computational Chemogenomics. Computational Chemogenomics 327 337 .

Tomoki Nakagawa, Tomoyuki Miyao & Kimito Funatsu. (2017) Identification of Bioactive Scaffolds Based on QSAR Models. Molecular Informatics 37:1-2.
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Carmen Cerchia, Dilyana Dimova, Antonio Lavecchia & Jürgen Bajorath. (2017) Exploring Structural Relationships between Bioactive and Commercial Chemical Space and Developing Target Hypotheses for Compound Acquisition. ACS Omega 2:11, pages 7760-7766.
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Dilyana Dimova & Jürgen Bajorath. (2017) Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?. Journal of Computer-Aided Molecular Design 31:7, pages 603-608.
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Dilyana Dimova & Jürgen Bajorath. (2017) Assessing Scaffold Diversity of Kinase Inhibitors Using Alternative Scaffold Concepts and Estimating the Scaffold Hopping Potential for Different Kinases. Molecules 22:5, pages 730.
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Jürgen Bajorath. (2017) Computational scaffold hopping: cornerstone for the future of drug design?. Future Medicinal Chemistry 9:7, pages 629-631.
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Ryo Kunimoto, Dilyana Dimova & Jürgen Bajorath. (2017) Application of a New Scaffold Concept for Computational Target Deconvolution of Chemical Cancer Cell Line Screens. ACS Omega 2:4, pages 1463-1468.
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Ye Hu, Dagmar Stumpfe & Jürgen Bajorath. (2016) Recent Advances in Scaffold Hopping. Journal of Medicinal Chemistry 60:4, pages 1238-1246.
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Dagmar Stumpfe, Dilyana Dimova & Jürgen Bajorath. (2017) Systematic analysis of structural and activity relationships between conventional hierarchical and analog series-based scaffolds. RSC Advances 7:30, pages 18718-18723.
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Analog Series-Based Scaffolds: Computational Design and Exploration of a New Type of Molecular Scaffolds for Medicinal Chemistry

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Analog Series-Based Scaffolds: Computational Design and Exploration of a New Type of Molecular Scaffolds for Medicinal Chemistry

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