PDB‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract

The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration (http://pdb101.rcsb.org). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Profile of Myracrodruon urundeuva Volatile Compounds Ease of Extraction and Biodegradability and In Silico Evaluation of Their Interactions with COX-1 and iNOS

“…Structure- based virtual screening applying docking simulations was performed using the AutoDock Vina tool [ 64 ]. The respective structures for each target were obtained from the protein data bank [ 65 ] or modeled by homology. The human COX-1 was modeled from the correspondent human sequence obtained from UniProt [ 66 ] using the tool Swiss-Model [ 67 ] and the ovine structure at the PDB-ID:1DIY (originally complexed to the arachidonic acid substrate).…”

Network Pharmacology and Bioinformatics Analyses Identify Intersection Genes of Vitamin D3 and COVID-19 as Potential Therapeutic Targets

“…The protein structures of COVID-19 associated proteins and target proteins were obtained from the PDB database ( https://www.rcsb.org/ ) ( Zardecki et al, 2022 ). The molecular structures of VD3 and Calcitriol were obtained from the PubChem database ( https://pubchem.ncbi.nlm.nih.gov/ ) ( Li et al, 2021a ).…”

Network pharmacology and experimental validation identify the potential mechanism of sophocarpine for COVID-19

“…The three-dimensional (3D) structures of SOP were obtained from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). The crystal structures of the targeted protein were searched in the Uniprot database [17] (https://www.uniprot.org/) and downloaded in PDB format in the RCSB Protein Data Bank database [18] (https://www.pdbus.org/). Autodock (version 4.2.6) was used to add polar hydrogen and set the grid box [19], and the autodock vina function was then run to perform molecular docking analysis.…”