PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds.

Tytuł:: PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds.
Autorzy:: Valdés-Jiménez A; Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile.
Peña-Varas C; Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile.
Borrego-Muñoz P; Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Campus Nueva Granada, Universidad Militar Nueva Granada, Cajicá 250247, Colombia.
Arrue L; Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile.
Alegría-Arcos M; Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile.
Nour-Eldin H; DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1017 Copenhagen, Denmark.
Dreyer I; Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile.
Nuñez-Vivanco G; Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile.
Ramírez D; Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile.
Źródło:: Molecules (Basel, Switzerland) [Molecules] 2021 Feb 20; Vol. 26 (4). Date of Electronic Publication: 2021 Feb 20.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Original Publication: Basel, Switzerland : MDPI, c1995-
MeSH Terms:: Databases, Chemical*
Phytochemicals/*chemistry
Plants/*chemistry
Molecular Docking Simulation ; Phytochemicals/metabolism ; Plants/metabolism ; Quantitative Structure-Activity Relationship
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Grant Information:: 11180604 Fondo Nacional de Desarrollo Científico y Tecnológico; 1150054 Fondo Nacional de Desarrollo Científico y Tecnológico; REDES190025 Comisión Nacional de Investigación Científica y Tecnológica
Contributed Indexing:: Keywords: 3D-structures; chemical and structural properties; database; natural products; physicochemical and pharmaceutical descriptors; plant secondary metabolites
Substance Nomenclature:: 0 (Phytochemicals)
Entry Date(s):: Date Created: 20210306 Date Completed: 20210407 Latest Revision: 20240331
Update Code:: 20240331
PubMed Central ID:: PMC7924326
DOI:: 10.3390/molecules26041124
PMID:: 33672700
: Czasopismo naukowe

Pełny tekst

Plants synthesize a large number of natural products, many of which are bioactive and have practical values as well as commercial potential. To explore this vast structural diversity, we present PSC-db, a unique plant metabolite database aimed to categorize the diverse phytochemical space by providing 3D-structural information along with physicochemical and pharmaceutical properties of the most relevant natural products. PSC-db may be utilized, for example, in qualitative estimation of biological activities (Quantitative Structure-Activity Relationship, QSAR) or massive docking campaigns to identify new bioactive compounds, as well as potential binding sites in target proteins. PSC-db has been implemented using the open-source PostgreSQL database platform where all compounds with their complementary and calculated information (classification, redundant names, unique IDs, physicochemical properties, etc.) were hierarchically organized. The source organism for each compound, as well as its biological activities against protein targets, cell lines and different organism were also included. PSC-db is freely available for public use and is hosted at the Universidad de Talca.

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