Author Archives: Ben Williams

Exploring the Protein Data Bank programmatically

The Worldwide Protein Data Bank (wwPDB or just the PDB to its friends) is a key resource for structural biology, providing a single central repository of protein and nucleic acid structure data. Most researchers interact with the PDB either by downloading and parsing individual entries as mmCIF files (or as legacy PDB files), or by downloading aggregated data, such as the RCSB‘s collection in a single FASTA file of all polymer entity sequences. All too often, researchers end up laboriously writing their own file parsers to digest these files. In recent years though, more sophisticated tools have been made available that make it much easier to access only the data that you need.

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