Biochem 301: Structural & Physical Biochemistry

Primary research: Original, peer-reviewed publication of a scientist’s new research and theories. Often includes intro, methods, results, discussion sections.

Secondary research: Literature source that cites, builds on, discusses, or generalizes primary sources (e.g., a review article).

Take a look at the papers linked below. Are they primary or secondary research articles? How do you know?

1. https://browzine.com/articles/389303573
2. https://bit.ly/3d3FUA5

Protein Data Bank (PDB): The single, worldwide repository of information about 3D structures of large biological molecules. RCSB PDB is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC. Includes a drug and drug target search, a comprehensive advanced search, and the capability to browse by annotations.

Universal Protein Resource (UniProt): A comprehensive resource for protein sequence and annotation data. UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR).

Entrez: Search across many National Center for Biotechnology Information (NCBI) databases at once using this federated search engine. Includes protein, nucleotide, and genome sequence databases.

ENZYME: A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

DrugBank: A unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. DrugBank is supported by the Canadian Institutes of Health Research. While not a structure or sequence database, it can be used to quickly look up drug targets, enzymes, and transporters to use in searching the above databases.

LIPID MAPS Lipidomics Gateway: Largest curated lipid structure database in the world. Funded by the Wellcome Trust and managed by researchers at Cardiff University, the Babraham Institute, and UC San Diego.

ChEMBL: A manually curated database of bioactive molecules with drug-like properties, ChEMBL brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Maintained by the European Bioinformatics Institute, part of the European Molecular Biology Laboratory (EMBL-EBI).

Cambridge Structural Database (CSD): Largest repository of experimentally determined organic and metal-organic crystal structures. Maintained by the Cambridge Crystallographic Data Centre (CCDC).

Inorganic Crystal Structure Database (ICSD): Largest database for completely determined inorganic crystal structures, provided by FIZ Karlsruhe - Liebniz-Institut für Informationsinfrastruktur.

Plant Metabolic Network (PMN): PMN currently houses one multi-species reference database called PlantCyc and 100 species/taxon-specific databases. PlantCyc provides access to manually curated or reviewed information about shared and unique metabolic pathways present in over 350 plant species.