Scientific Databases
Layered by data versus tools. The biology group runs from proteins to pathways: sequence and function annotation in UniProt and Gene Ontology, 3D structures in RCSB PDB, expression and localization in the Human Protein Atlas, pathway analysis with KEGG and Reactome, gene-list enrichment through Metascape, and mass-spectrometry proteomics data via ProteomeXchange and PRIDE — the entries to use when a journal requires data deposition; EMBL-EBI is the parent portal for many of them. The chemistry group is calculation-centred: ChemCalc parses formulae and computes molecular weights, and the NIST glyco mass calculator pairs with MS data. The calculator group holds the tools that live next to the bench — hydropathy, peptide masses, fragment ions and gel concentrations — plus MDCalc for medical formulas. Search databases by accession or PDB ID first, which beats keywords; and when feeding sequences to calculators, check termini and modification settings or the numbers will not mean much.
