Brazilian Biodiversity Natural Products Database: BrNPDB
Resumo
Released in 2013, the NuBBEDB is one of the best sources of natural products from Brazilian biodiversity. However, new possibilities have emerged with advances in scientific research and technologies. In this study, we demonstrate and discuss the development of the Brazilian Biodiversity Natural Products Database (BrNPDB), the relevance of Natural Products databases in Brazil, the materials and methods for data modeling, integration, standards and generated data from the cutting-edge sources, applications and technologies. The results show how BrNPDB upgrades NuBBEDB in many ways and contributes to the growing demand for platforms that enable more effective integration of chemical, biological, and ecological data.
Palavras-chave:
Natural Products, Databases, Biodiversity, Cheminformatics, Drug Discovery
Referências
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Van Santen J. A., Jacob, G. et al. (2019). “The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”. ACS Central Science 2019 5 (11), 1824-1833
Waagmeester, A.; Schriml, L., Su, A. (2019). “Wikidata as a linked-data hub for Biodiversity data”. Biodiversity Information Science and Standards, 3, e35206, 2019.
Xue, R., Fang, Z. et al (2013). "TCMID: Traditional Chinese medicine integrative database for herb molecular mechanism analysis". Nucleic Acids Res., 41, D1089–D1095.
Zdrazil, B., Felix, E. et al (2024). “The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods”, Nucleic Acids Research, Volume 52, Issue D1, Pages D1180–D1192.
Zhang, Y., Jin, H., et al. (2024). “A comprehensive survey on process-oriented automatic text summarization with exploration of llm-based methods.” arXiv preprint, arXiv:2403.02901.
Bánki, O., Roskov, Y. et al. (2025). “Catalogue of Life (Version 2025-07-10)”. Catalogue of Life Foundation, Amsterdam, Netherlands.
Calixto, J. B. (2019). “The role of natural products in modern drug discovery”. Anais da Academia Brasileira de Ciências, v. 91, n.3.
Cao Y., Charisi A., et al. (2008). “ChemmineR: a compound mining framework for R.” Bioinformatics, 24 (15), 1733–1734.
Chang W., Cheng J. et al. (2025). “Shiny: Web Application Framework for R”. R package version 1.11.1.9000
Chen, C.Y.-C (2011). "TCM Database@Taiwan: The world’s largest traditional Chinese medicine database for drug screening in silico". PLoS ONE, 6, e15939.
Gaudry, A., Pagni, M., et al (2024). “A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery”. ACS Cent Sci. 2024 Feb 20;10(3):494-510.
Gómez-García, A., Jiménez, D. A. A. et al. (2024). “Latin American Natural Product Database (LANaPDB): An Update”, In: J. Chem. Inf. Model. 64 (22), 8495-8509
Guha, R. (2007). “Chemical Informatics Functionality in R.” J. of Stat. Software, 18
Hatherley, R., Brown, D. K. et al (2015). "SANCDB: A South African natural compound database". J. Cheminform., 7, 29.
Jumper, J. et al. (2021) "Highly accurate protein structure prediction with AlphaFold." Nature 596, 583–589
Kim S., Chen J., Cheng T., et al. (2025). “PubChem 2025 update”. Nucleic Acids Res. 2025;53(D1): D1516-D1525.
Kim, H.W., Wang, M. et al (2021). “NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products”. J. Nat. Prod., 84, 2795–2807
Kim, S. K., Nam, S. et al (2015). “TM-MC: A database of medicinal materials and chemical compounds in Northeast Asian traditional medicine”. BMC Complement. Altern. Med., 15, 218.
Marx E., Schmidt-Dichte S. and Mocsy I. J. (2023). “nubbe: The data model for nubbeDB Knowledge Graph”. [link]
Meijer, D., Beniddir, M. A. et al (2024). “Empowering natural product science with AI: leveraging multimodal data and knowledge graphs”, Royal Society of Chemistry, Nat. Prod. Rep.
Newman, D. J., Cragg, G. M. (2020). “Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019”. Journal of Natural Products, 27,83(3), 770-883.
Ntie-Kang, F., Telukunta, K.K. et al (2017). "NANPDB: A Resource for Natural Products from Northern African Sources". J. Nat. Prod., 80, 2067–2076.
O'Boyle, N. M., Banck, M., et al (2011). “Open Babel: An open chemical toolbox”. J Cheminform 3, 33.
Pilon, A., Valli, M., et al. (2017). “NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity”, In: Scientific Reports | 7: 7215
R Core Team (2024). “R: A Language and Environment for Statistical Computing”. R Foundation for Stat. Computing, Vienna, Austria.
Rajan, K., Zielesny, A., and Steinbeck, C. (2022). “STOUT-V2 (2.0.0)”. Zenodo.
Saldívar-González, F. I., Aldas-Bulos, V. D., et al. (2022). “Natural product drug discovery in the artificial intelligence era”, Chem. Sci., 13, 1526-1546.
Scotti, M.T., Herrera-Acevedo, C. et al (2018). “SistematX, an OnlineWeb-Based Cheminformatics Tool for Data Management of Secondary Metabolites”. Molecules, 23, 103
Sorokina, M., Steinbeck, C. (2020). “Review on natural products databases: where to find data in 2020”. J. Cheminform 12, 20.
Steinbeck C., Chandrasekhar V., Rajan K., et al. (2025). “COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database”. Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D634–D643
Thessen, A. E., Patterson, D. J. (2011). “Data issues in the life sciences”. ZooKeys, v. 150, p. 15-51.
Valli, M., dos Santos, R. N. et al (2013). "Development of a natural products database from the biodiversity of Brazil". J. Nat. Prod., 76, 439–444.
Van Santen J. A., Jacob, G. et al. (2019). “The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”. ACS Central Science 2019 5 (11), 1824-1833
Waagmeester, A.; Schriml, L., Su, A. (2019). “Wikidata as a linked-data hub for Biodiversity data”. Biodiversity Information Science and Standards, 3, e35206, 2019.
Xue, R., Fang, Z. et al (2013). "TCMID: Traditional Chinese medicine integrative database for herb molecular mechanism analysis". Nucleic Acids Res., 41, D1089–D1095.
Zdrazil, B., Felix, E. et al (2024). “The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods”, Nucleic Acids Research, Volume 52, Issue D1, Pages D1180–D1192.
Zhang, Y., Jin, H., et al. (2024). “A comprehensive survey on process-oriented automatic text summarization with exploration of llm-based methods.” arXiv preprint, arXiv:2403.02901.
Publicado
29/09/2025
Como Citar
NEVES, Fillipe A. et al.
Brazilian Biodiversity Natural Products Database: BrNPDB. In: SIMPÓSIO BRASILEIRO DE BIOINFORMÁTICA (BSB), 18. , 2025, Fortaleza/CE.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2025
.
p. 37-47.
ISSN 2316-1248.
DOI: https://doi.org/10.5753/bsb.2025.15135.
