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Leal CM, Leitão SG, Sausset R, Mendonça SC, Nascimento PHA, de Araujo R. Cheohen CF, Esteves MEA, Leal da Silva M, Gondim TS, Monteiro MES, Tucci AR, Fintelman-Rodrigues N, Siqueira MM, Miranda MD, Costa FN, Simas RC, Leitão GG. Flavonoids from Siparuna cristata as Potential Inhibitors of SARS-CoV-2 Replication. REVISTA BRASILEIRA DE FARMACOGNOSIA : ORGAO OFICIAL DA SOCIEDADE BRASILEIRA DE FARMACOGNOSIA 2021; 31:658-666. [PMID: 34305198 PMCID: PMC8294293 DOI: 10.1007/s43450-021-00162-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/03/2021] [Indexed: 11/15/2022]
Abstract
The novel coronavirus SARS-CoV-2 has been affecting the world, causing severe pneumonia and acute respiratory syndrome, leading people to death. Therefore, the search for anti-SARS-CoV-2 compounds is pivotal for public health. Natural products may present sources of bioactive compounds; among them, flavonoids are known in literature for their antiviral activity. Siparuna species are used in Brazilian folk medicine for the treatment of colds and flu. This work describes the isolation of 3,3',4'-tri-O-methyl-quercetin, 3,7,3',4'-tetra-O-methyl-quercetin (retusin), and 3,7-di-O-methyl-kaempferol (kumatakenin) from the dichloromethane extract of leaves of Siparuna cristata (Poepp. & Endl.) A.DC., Siparunaceae, using high-speed countercurrent chromatography in addition to the investigation of their inhibitory effect against SARS-CoV-2 viral replication. Retusin and kumatakenin inhibited SARS-CoV-2 replication in Vero E6 and Calu-3 cells, with a selective index greater than lopinavir/ritonavir and chloroquine, used as control. Flavonoids and their derivatives may stand for target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections. GRAPHICAL ABSTRACT SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s43450-021-00162-5.
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Affiliation(s)
- Carla Monteiro Leal
- Programa de Pós-graduação em Biotecnologia Vegetal e Bioprocessos, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
| | - Suzana Guimarães Leitão
- Faculdade de Farmácia, Centro de Ciências da Saúde, Bl. A 2º andar, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
| | - Romain Sausset
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
- Muséum National D’Histoire Naturelle, 75005 Paris, France
| | - Simony C. Mendonça
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
| | - Pedro H. A. Nascimento
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
| | - Caio Felipe de Araujo R. Cheohen
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965-045 Brazil
| | - Maria Eduarda A. Esteves
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041-361 Brazil
| | - Manuela Leal da Silva
- Programa de Pós-graduação Multicêntrico em Ciências Fisiológicas, Centro de Ciências da Saúde, Instituto de Biodiversidade e Sustentabilidade NUPEM, Universidade Federal do Rio de Janeiro, Macaé, RJ 27965-045 Brazil
- Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, RJ 21041-361 Brazil
| | - Tayssa Santos Gondim
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
| | - Maria Eduarda S. Monteiro
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
| | - Amanda Resende Tucci
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
| | - Natália Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
- Instituto Nacional de Ciência e Tecnologia de Gestão da Inovação em Doenças Negligenciadas, Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21041-210 Brazil
| | - Marilda M. Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
| | - Milene Dias Miranda
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, 21041-210 Brazil
| | - Fernanda N. Costa
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
| | - Rosineide C. Simas
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, GO 74690-900 Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Centro de Ciências da Saúde, Bl. H, Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902 Brazil
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Ragno R. www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices—the Py-CoMFA web application as tool to build models from pre-aligned datasets. J Comput Aided Mol Des 2019; 33:855-864. [DOI: 10.1007/s10822-019-00231-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/28/2019] [Indexed: 11/28/2022]
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Erkimbaev AO, Zitserman VY, Kobzev GA, Serebrjakov VA, Teymurazov KB. Publishing scientific data as linked open data. SCIENTIFIC AND TECHNICAL INFORMATION PROCESSING 2014. [DOI: 10.3103/s014768821304014x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Maeda MH, Kondo K. Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures. J Chem Inf Model 2013; 53:527-33. [PMID: 23293959 DOI: 10.1021/ci300309k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A database of 3D structures of natural metabolites has been developed called 3DMET. During the process of structure conversion from 2D to 3D, we found many structures were misconverted at chiral atoms and bonds. Several popular converters were tested in regard to their conversion accuracy. For verification, three canonical strings were also tested. No procedure could satisfactorily cover all the structures of the natural products. The misconverted structures had to be corrected manually. However, a nonnegligible number of mistakes were also observed even after manual curation, so a self-checking system was developed and introduced to our work flow. Thus, the 3D structures in our 3DMET database were evaluated in two steps: automatically and manually. The current version includes most of the natural products of the KEGG COMPOUND collection [ http://www.genome.jp/kegg/compound/ ] and is searchable by string, value range, and substructure. 3DMET can be accessed via http://www.3dmet.dna.affrc.go.jp/ , which also has detailed manuals.
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Affiliation(s)
- Miki H Maeda
- Biomolecular Research Unit, National Institute of Agrobiological Sciences , 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Warr WA. Silver threads. J Comput Aided Mol Des 2011; 26:151-2. [PMID: 22160657 DOI: 10.1007/s10822-011-9502-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 11/29/2011] [Indexed: 11/27/2022]
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Murray-Rust P, Adams SE, Downing J, Townsend JA, Zhang Y. The semantic architecture of the World-Wide Molecular Matrix (WWMM). J Cheminform 2011; 3:42. [PMID: 21999475 PMCID: PMC3205046 DOI: 10.1186/1758-2946-3-42] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 10/14/2011] [Indexed: 12/02/2022] Open
Abstract
The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.
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Affiliation(s)
- Peter Murray-Rust
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Sam E Adams
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jim Downing
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Joe A Townsend
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Yong Zhang
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
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Abstract
Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured.
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Willighagen EL, Brändle MP. Resource description framework technologies in chemistry. J Cheminform 2011; 3:15. [PMID: 21569523 PMCID: PMC3118380 DOI: 10.1186/1758-2946-3-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 05/13/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Egon L Willighagen
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden.
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9
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Warr WA. Representation of chemical structures. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.36] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics 2010; 9:1703-15. [PMID: 20525940 DOI: 10.1074/mcp.r000007-mcp201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linking proteomics and structural data is critical to our understanding of cellular processes, and interactive exploration of these complementary data sets can be extremely valuable for developing or confirming hypotheses in silico. However, few computational tools facilitate linking these types of data interactively. In addition, the tools that do exist are neither well understood nor widely used by the proteomics or structural biology communities. We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data.
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Affiliation(s)
- John H Morris
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
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Zhang ZM, Chen S, Liang YZ. A novel storage method for near infrared spectroscopy chemometric models. Anal Chim Acta 2010; 668:149-54. [PMID: 20493291 DOI: 10.1016/j.aca.2010.04.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 04/15/2010] [Accepted: 04/15/2010] [Indexed: 11/28/2022]
Abstract
Chemometric Modeling Markup Language (CMML) is developed by us for containing chemometrics models within one document through converting binary data into strings by base64 encode/decode algorithms to solve the interoperability issue in sharing chemometrics models. It provides a base functionality for storage of sampling, variable selection, pretreating, outlier and modeling parameters and data. With the help of base64 algorithm, the usability of CMML is in equilibrium with size by transforming the binary data into base64 encoded string. Due to the advantages of Extensible Markup Language (XML), models stored in CMML can be easily reused in various other software and programming languages as long as the programming language has XML parsing library. One can also use the XML Path Language (XPath) query language to select desired data from the CMML file effectively. The application of this language in near infrared spectroscopy model storage is implemented as a class in C++ language and available as open source software (http://code.google.com/p/cmml), and the implementations in other languages, such as MATLAB and R are in progress.
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Affiliation(s)
- Zhi-Min Zhang
- College of Chemistry and Chemical Engineering, Research Center of Modernization of Chinese Medicines, Central South University, Changsha 410083, PR China
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Adams N, Winter J, Murray-Rust P, Rzepa HS. Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. J Chem Inf Model 2008; 48:2118-28. [DOI: 10.1021/ci8002123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nico Adams
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Jerry Winter
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Peter Murray-Rust
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Henry S. Rzepa
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
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Adams N, Murray-Rust P. Engineering Polymer Informatics: Towards the Computer-Aided Design of Polymers. Macromol Rapid Commun 2008. [DOI: 10.1002/marc.200700832] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Ashino T, Bartolo L. Seminar Cum Meeting Report: Codata Task Group for Exchangeable Material Data Representation to Support Research and Education. DATA SCIENCE JOURNAL 2008. [DOI: 10.2481/dsj.7.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kuhn S, Helmus T, Lancashire RJ, Murray-Rust P, Rzepa HS, Steinbeck C, Willighagen EL. Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data. J Chem Inf Model 2007; 47:2015-34. [PMID: 17887743 DOI: 10.1021/ci600531a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist.
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Affiliation(s)
- Stefan Kuhn
- Cologne University Bioinformatics Center (CUBIC), Cologne, Germany
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Dong X, Gilbert KE, Guha R, Heiland R, Kim J, Pierce ME, Fox GC, Wild DJ. Web service infrastructure for chemoinformatics. J Chem Inf Model 2007; 47:1303-7. [PMID: 17602467 DOI: 10.1021/ci6004349] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.
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Affiliation(s)
- Xiao Dong
- Indiana University School of Informatics, Community Grids Laboratory, and Chemical Informatics and Cyberinfrastructure Collaboratory, Indiana University, Bloomington, Indiana 47408, USA
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Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JES. Bioclipse: an open source workbench for chemo- and bioinformatics. BMC Bioinformatics 2007; 8:59. [PMID: 17316423 PMCID: PMC1808478 DOI: 10.1186/1471-2105-8-59] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 02/22/2007] [Indexed: 11/13/2022] Open
Abstract
Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at .
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Affiliation(s)
- Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Tobias Helmus
- Cologne University Bioinformatics Center, Cologne University, Cologne, Germany
| | - Egon L Willighagen
- Cologne University Bioinformatics Center, Cologne University, Cologne, Germany
| | - Stefan Kuhn
- Cologne University Bioinformatics Center, Cologne University, Cologne, Germany
| | - Martin Eklund
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | - Peter Murray-Rust
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, UK
| | - Christoph Steinbeck
- Cologne University Bioinformatics Center, Cologne University, Cologne, Germany
| | - Jarl ES Wikberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Taylor KR, Gledhill RJ, Essex JW, Frey JG, Harris SW, De Roure DC. Bringing Chemical Data onto the Semantic Web. J Chem Inf Model 2006; 46:939-52. [PMID: 16711712 DOI: 10.1021/ci050378m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Present chemical data storage methodologies place many restrictions on the use of the stored data. The absence of sufficient high-quality metadata prevents intelligent computer access to the data without human intervention. This creates barriers to the automation of data mining in activities such as quantitative structure-activity relationship modelling. The application of Semantic Web technologies to chemical data is shown to reduce these limitations. The use of unique identifiers and relationships (represented as uniform resource identifiers, URIs, and resource description framework, RDF) held in a triplestore provides for greater detail and flexibility in the sharing and storage of molecular structures and properties.
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Affiliation(s)
- K R Taylor
- School of Chemistry, University of Southampton, SO17 1BJ United Kingdom
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21
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Rousay ER, Fu H, Robinson JM, Essex JW, Frey JG. Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:2075-95. [PMID: 16099767 DOI: 10.1098/rsta.2005.1630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Conventional paper-based scientific publications are limited in the amount of data and interaction they can provide. Simply placing an electronic copy of such a publication on the web makes for easier distribution, but more can be achieved by making use of the technology to navigate through the paper, to show the links between calculated parameters and the data, and provide access to the chain of calculated results all the way back to the raw data and ultimately the laboratory notebook. While the paper version of this publication is in a relatively conventional form, an interactive demonstrator version (available at http://epaper.combe.chem.soton.ac.uk and as an installable package) illustrates the concepts of publication@source, whereby all the figures and data presented in the paper are linked back to the original raw data together with a description of the processes by which the raw data were analysed. This level of interactivity is achieved using semantic technologies, which have the additional advantage of making the final document subsequently available and navigable by automated techniques. We present the combined information from experimental studies of surface tension and second harmonic generation (SHG) on the behaviour of benzo-15-crown-5 at the solution/air interface, together with a molecular dynamics computer simulation, to demonstrate how the simulation aids the interpretation of the SHG experiment. The adsorption isotherm was determined using SHG and fitted to a Langmuir isotherm giving Delta ads G0=26 kJ mol-1.
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Affiliation(s)
- Esther R Rousay
- School of Chemistry, University of Southampton, Highfield, Southampton, UK
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Murray-Rust P, Rzepa HS, Stewart JJP, Zhang Y. A global resource for computational chemistry. J Mol Model 2005; 11:532-41. [PMID: 16086187 DOI: 10.1007/s00894-005-0278-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 05/02/2005] [Indexed: 11/25/2022]
Abstract
A modular distributable system has been built for high-throughput computation of molecular structures and properties. It has been used to process 250,000 compounds from the NCI database and to make the results searchable by structures and properties. The IUPAC/NIST InChI specification and algorithm has been used to index the structures and enforce integrity during computation. A number of novel features of the PM5 Hamiltonian were identified as a result of the high-throughput approach. The system and the data can be redistributed and reused and promote the value of computed data as a primary chemical resource.
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Affiliation(s)
- Peter Murray-Rust
- Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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Donald JE, Hubner IA, Rotemberg VM, Shakhnovich EI, Mirny LA. CoC: a database of universally conserved residues in protein folds. Bioinformatics 2005; 21:2539-40. [PMID: 15746286 DOI: 10.1093/bioinformatics/bti360] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
UNLABELLED The conservatism of conservatism (CoC) database presents statistically analyzed information about the conservation of residue positions in folds across protein families. AVAILABILITY On the web at http://kulibin.mit.edu/coc/
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Affiliation(s)
- Jason E Donald
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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