structure-db

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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Provided by

anvi-gen-structure-database anvi-update-structure-database

Required by

anvi-display-structure anvi-export-structures anvi-update-structure-database

Can be used by

anvi-db-info anvi-gen-fixation-index-matrix anvi-gen-variability-profile anvi-migrate

Description

This database contains the protein structural data for genes in a corresponding contigs-db and can be generated with anvi-gen-structure-database.

The structures can be predicted with either template-based homology modelling (MODELLER) or AlphaFold2 (ColabFold), or imported from pre-computed structures you provide. The database records which engine was used, along with that engine’s confidence metrics: MODELLER’s DOPE/GA341/molpdf scores, or ColabFold’s per-residue pLDDT and model-level pTM.

Currently, this database is best utilized for visualizing 3D structures with anvi-display-structure.

For more information on the structure database, see this blog post.

This artifact is currently a stub. I’m looking at you, Evan. - Evan

Edit this file to update this information.