The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.
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http://dx.doi.org/10.1002/pro.3331 | DOI Listing |
Methods Mol Biol
January 2025
Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
While traditional assay methods face challenges in detecting specific proteins, aptamers, known for their high specificity and affinity, are emerging as a valuable biomarker detection tool. Aurora kinase A (AURKA) plays a role in cell division and influences stem cell reprogramming. In this study, an in silico approach method was conducted for a random ssDNA aptamer sequence selection and its binding with AURKA.
View Article and Find Full Text PDFOpen Vet J
November 2024
Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia.
Background: Snake venoms are mainly composed of a mixture of proteins and peptides with antiviral activity against several viruses including HIV. Therefore, snake venoms represent a promising source for new antiviral drugs.
Aim: The study examines the toxin's capacity to disrupt the spike glycoprotein of HIV, the virus accountable for the HIV epidemic.
J Diabetes Metab Disord
December 2024
Laboratoire des Sciences Fondamentales, Université Amar Telidji, Laghouat, BP37G Algeria.
Aims: Desf. (Anacardiaceae) is traditionally used in Mediterranean medicine, with previous studies showing antidiabetic potential in its fruits and leaves. This study evaluates the antidiabetic activity of galls (PAG) extracts using in vitro, chemometric, and in silico approaches.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.
View Article and Find Full Text PDFCurr Opin Struct Biol
November 2024
Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, CA 92093, USA; Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address:
Structural biologists and the open-access Protein Data Bank (PDB) played decisive roles in combating the COVID-19 pandemic. Global biostructure data were turned into global knowledge, allowing scientists and engineers to understand the inner workings of coronaviruses and develop effective countermeasures. Two mRNA vaccines, initially designed with guidance from PDB structures of the SARS-CoV-1 and MERS-CoV spike proteins, prevented infections entirely or reduced the likelihood of morbidity and mortality for more than five billion individual recipients worldwide.
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