PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within PubChem. These web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure-activity analysis, and target selectivity examination. This article reviews these bioactivity analysis tools and discusses their uses. Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703903 | PMC |
| http://dx.doi.org/10.1093/nar/gkp456 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Evaluation of the Recent Dynamics for Funding Medicinal Chemistry Projects in Academia. Results of a Survey Conducted by IUPAC Division VII (Chemistry and Human Health).
J Med Chem
January 2025
Department of Chemistry, Faculty of the Exact Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
Data collected from scholars across twenty-three countries over the past decade (2010-2019) reveals a 40% decrease in financial support for medicinal chemistry projects. The decline is especially notable among projects focused on small organic molecules. This drop in grants indicates a troubling trend that could jeopardize future drug development by undermining research in this crucial field.
View Article and Find Full Text PDFSerine phosphorylation facilitates protein degradation by the human mitochondrial ClpXP protease.
Proc Natl Acad Sci U S A
February 2025
Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
ClpXP is a two-component mitochondrial matrix protease. The caseinolytic mitochondrial matrix peptidase chaperone subunit X (ClpX) recognizes and translocates protein substrates into the degradation chamber of the caseinolytic protease P (ClpP) for proteolysis. ClpXP degrades damaged respiratory chain proteins and is necessary for cancer cell survival.
View Article and Find Full Text PDFUnraveling Ofloxacin Behavior in Aqueous Environments: Molecular Dynamics of Colloidal Formation and Surface Adsorption Mechanisms.
Langmuir
January 2025
School of Chemical Engineering, The University of Queensland, Brisbane, QLD 4072, Australia.
Ofloxacin, a commonly prescribed antibiotic, raises serious environmental concerns due to its persistence in aquatic systems. This study offers new insights into the environmental behavior of ofloxacin and its interactions with carbon-based adsorbents with the aim of enhancing our understanding of its removal mechanisms via adsorption processes. Using a comprehensive computational approach, we analyzed the speciation, pK values, and solubility of ofloxacin across various pH conditions, accounting for all four microspecies, including the often-overlooked neutral form.
View Article and Find Full Text PDFSmall Molecule Modulators of AMP-Activated Protein Kinase (AMPK) Activity and Their Potential in Cancer Therapy.
J Med Chem
January 2025
Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, Aurora, Colorado 80045, United States.
AMP-activated protein kinase (AMPK) is a central mediator of cellular metabolism and is activated in direct response to low ATP levels. Activated AMPK inhibits anabolic pathways and promotes catabolic activities that generate ATP through the phosphorylation of multiple target substrates. AMPK is a therapeutic target for activation in several chronic metabolic diseases, and there is increasing interest in targeting AMPK activity in cancer where it can act as a tumor suppressor or conversely it can support cancer cell survival.
View Article and Find Full Text PDFDesign strategies and biomedical applications of organic NIR-IIb fluorophores.
Chem Commun (Camb)
January 2025
Marshall Laboratory of Biomedical Engineering, International Cancer Center, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, China.
The introduction of fluorescence imaging (FLI) in near-infrared II sub-channels (NIR-IIb, 1500-1700 nm) has revolutionized the ability to explore complex patho-physiological settings . Despite the transformative potentials, the development of organic NIR IIb dyes encounters considerable difficulties, and only a limited number of such fluorophores have been developed so far. This review systematically introduces design strategies of organic NIR-IIb fluorophores classified by molecular scaffolds, mainly including cyanine dyes and D-A-D small molecule dyes.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!