Microbial 'omics

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pdb-db [artifact]

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A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Required or used by



What is this thing?

This is a comprehensive database of protein structures downloaded from the PDB RSCB that are non-redundant. Currently, it is used for those who want to run anvi-gen-structure-database without an internet connection.

Where does it come from?

A pdb-db can be created via the program anvi-setup-pdb-database. Alternatively, a pdb-db that contains custom structures not found in the RCSB PDB can in theory be generated by the user, but anvi’o currrently offers no reasonable way of doing this.


The pdb-db generated via anvi-setup-pdb-database is ~20GB.

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