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PubChem can be availed through the NCBI Entrez system. In Entrez’s PubChem Compound database, one can search a compound with a chemical synonym, and also link to a list of screening experiments including the given compound via the ‘BioAssays’ link. One can also find, all bioassay tests for a specific target by querying protein target name.
The PubChem Pathway collection was constructed with records from multiple pathway information resources, including Reactome, 16 Plant Reactome, 17 BioCyc, 18 PlantCyc, 19 WikiPathways, 20 PathBank, 21 LIPID MAPS, 22 PharmGKB, 23 Pathway Interaction Database, 24 INOH 25 and the COVID-19 Disease Map. 26 It is noteworthy that, while different data ...
Neighboring 3-D descriptions of PubChem Compound, much like the 2-D similarity neighbors currently available, may help scientists identify and better understand interrelationships of the biological properties of small molecules. It is, to this end, that a 3-D description of the PubChem Compound database is in progress.
In thisstudy, the PubChem database (nearly 10 million small molecules) was docked into the SHP2(PDB ID: 3O5X) binding site by the program Discovery Studio V3.5(DS). The binding site was defined based on the interaction between JZG and SHP2.
PubChem is the world's largest open-source database of chemical entities managed by the National Institutes of Health (NIH) [45] and can be accessed via https://pubchem.ncbi.nlm.nih.gov/. It was launched in 2004 and since then it has been serving as a key chemical information repository for students, scientists, as well as the general public.
The chemical structures were extracted from the PubChem database. The physicochemical properties of polyphenols such as miLogP, Hydrogen Bond Acceptor (HBA), Hydrogen Bond Donor (HBD), Molecular weight, Total Polar Surface Area (TPSA), Number of heavy atoms, Number of Rotatable Bonds, and Molecular volume (MV) were collected using ...
Vice versa, the same frequently used common plant or pharmaceutical names may be applied to different species. Therefore, we carefully distinguish the scientific and non-scientific common names to eradicate this problem. Besides this, SuperTCM provides (1) ingredient similarity search by connecting with the PubChem database [17]. (2) reliable ...
PubChem is an open-source database of chemical molecules that provides search facilities via name, structure, molecular formula, and other identifiers (such as CAS numbers). The database also provides the information regarding the physical characteristics, chemical properties, biological activities, safety and toxicity information of the molecules.
Another 216 articles that simply cited PubChem as one representative public chemical biology database or had little relevance to PubChem utilization were excluded as well. As a result, a total of 571 articles were excluded (Table S1 in the supplementary material online), and the remaining 1132 research articles were used for subsequent analysis ...
And considering that many P450s lack experimentally validated crystal structures, we have included hyperlinks to access predicted protein structures from the AlphaFold database. In terms of the substrate/product details, we collected the respective formulas, Smiles notation, and structures from the PubChem database.