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      TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine

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          Abstract

          Background

          In traditional medicine, there has been a great deal of research on the effects exhibited by medicinal materials. To study the effects, resources that can systematically describe the chemical compounds in medicinal materials are necessary. In recent years, numerous databases on medicinal materials and constituent compounds have been constructed. However, because these databases provide differing information and the sources of such information are unclear or difficult to verify, it is difficult to decide which database to use. Moreover, there is much overlapping information. The aim of this study was to construct a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine (TM-MC), for which medicinal materials are listed in the Korean, Chinese, and Japanese pharmacopoeias and information on the compound names of medicinal materials can easily be confirmed online.

          Description

          To provide information on the chemical compounds of medicinal materials, chromatography articles from MEDLINE and PubMed Central were searched. After chemical compounds of medicinal materials were extracted by manually investigating the full-text of articles, a database of information on about 14,000 compounds from 536 medicinal materials was built. The database also provides links to the articles from which each medicinal material and chemical compound were extracted.

          Conclusion

          TM-MC database provides information on medicinal materials and their chemical compounds from chromatography articles in MEDLINE and PubMed Central. Researchers can easily check relevant information through the links to articles.

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          Most cited references26

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          TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico

          Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.
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            NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database

            Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC50/ED50/EC50/GI50), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients’ Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI50 data.
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              Development of a natural products database from the biodiversity of Brazil.

              We describe herein the design and development of an innovative tool called the NuBBE database (NuBBEDB), a new Web-based database, which incorporates several classes of secondary metabolites and derivatives from the biodiversity of Brazil. This natural product database incorporates botanical, chemical, pharmacological, and toxicological compound information. The NuBBEDB provides specialized information to the worldwide scientific community and can serve as a useful tool for studies on the multidisciplinary interfaces related to chemistry and biology, including virtual screening, dereplication, metabolomics, and medicinal chemistry. The NuBBEDB site is at http://nubbe.iq.unesp.br/nubbeDB.html .
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                Author and article information

                Contributors
                snailee@kribb.re.kr
                Journal
                BMC Complement Altern Med
                BMC Complement Altern Med
                BMC Complementary and Alternative Medicine
                BioMed Central (London )
                1472-6882
                9 July 2015
                9 July 2015
                2015
                : 15
                : 218
                Affiliations
                [ ]Mibyeong Research Center, Korea Institute of Oriental Medicine, Daejeon, South Korea
                [ ]Biomedical Knowledge Engineering Laboratory, Seoul National University, Seoul, South Korea
                [ ]Human Derived Material Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
                Article
                758
                10.1186/s12906-015-0758-5
                4495939
                26156871
                528fbfb5-e281-4dc4-867e-8a1e44547292
                © Kim et al. 2015

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 14 April 2015
                : 1 July 2015
                Categories
                Database
                Custom metadata
                © The Author(s) 2015

                Complementary & Alternative medicine
                medicinal material,herb,chemical compound,ingredient,traditional medicine,northeast asia,chromatography,curation,database

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