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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.
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http://dx.doi.org/10.1093/nar/gkaa1038 | DOI Listing |
Curr Pharm Des
August 2025
King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
Introduction: Ovarian cancer (OC) is a malignancy of the female reproductive system for which cisplatin chemotherapy is one of the first-line treatments. Despite the initial response to chemotherapy, such patients eventually develop resistance, which poses a major obstacle to treatment, along with potential side effects. Phytochemicals function as chemosensitizers, offering novel therapies in OC patients by targeting drug resistance, and are perceived to be less toxic.
View Article and Find Full Text PDFJ Chem Inf Model
September 2025
Bioproduct Institute, Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
We introduce , a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS.
View Article and Find Full Text PDFNeotrop Entomol
September 2025
Department of Zoology, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia.
This study evaluated the larvicidal efficacy of the methanol extract of Dactyloctenium aegyptium against Aedes aegypti (L, 1762) (Diptera: Culicidae), Anopheles stephensi Liston, 1901 (Diptera: Culicidae), and Culex quinquefasciatus Say, 1823 (Diptera: Culicidae). The methanol extract exhibited the highest mortality rates, achieving 100% mortality at 250 µg/mL for all species tested, and demonstrated the lowest LC values of 94.28 µg/mL for Ae.
View Article and Find Full Text PDFExpert Rev Proteomics
September 2025
Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
Introduction: Targeted quantitative proteomics is vital for accurate protein measurement in biological samples. Techniques like Multiple Reaction Monitoring (MRM or SRM) and Parallel Reaction Monitoring (PRM), often used with isotopically-labeled internal standards, provide absolute quantification and represent the current gold standard. However, developing and validating assays for individual proteins remains labor-intensive.
View Article and Find Full Text PDFLife Sci Alliance
November 2025
Department of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
The mammalian target of rapamycin complex 1 (mTORC1) signaling pathway, composed of amino acid (AA)-sensing (Ragulator/LAMTOR-Rag) and growth factor (GF)-sensing (AKT-TSC1/2-Rheb) axes, pivotally regulates intracellular anabolism and catabolism. mTORC1 deregulation is associated with various metabolic diseases, including cancer and diabetes. As a key regulator of nutrient signaling, mTORC1 integrates a variety of nutrient signals.
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