PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search

PanRes is a structure-informed antimicrobial resistance database that integrates resistance genes, protein translations, predicted protein structures, structure-based clusters, multiple sequence alignments, and 3D-based Hidden Markov Models. The database can also be explored through the PanRes web service: https://panres.rambio.dk/ PanRes (version 2.0) includes the following files: File Description panres2_genes.fa FASTA file containing nucleotide sequences of PanRes genes. panres2_proteins.faa FASTA file containing translated protein sequences. PanGenes.tsv Metadata table for PanRes genes, including database origin and ontology relationships. PanProteins.tsv Metadata table for PanRes proteins, including links to genes, clusters, and structures where available. PanStructures.tsv Metadata table for predicted structures and structure-cluster membership. README_metadata.md Description of the metadata tables. panres2_ontology.owl OWL ontology file describing the PanRes data model and relationships. README_ontology.md Description of the PanRes ontology, including the main classes, object properties and annotation fields. PDBs.zip Predicted AlphaFold protein structures in PDB format, for example PAN1_struct.pdb. MSAs.zip Multiple sequence alignments for PanStructureClusters, used to build the HMM profiles, for example PANCL1_struct.full.aln.fasta. HMMs.zip Profile Hidden Markov Models for PanStructureClusters, for example PANCL1_struct.hmm. A number of previously published collections of AMR genes were used in the creation of the original PanRes gene collection bundled with ARGprofiler(See references): ResFinder (downloaded 2023-01-20, (Bortolaia et al. 2020)), ResFinderFG (version 2.0, (Gschwind et al. 2023)) CARD (version 3.2.5, (Alcock et al. 2023)) MegaRes (version 3.0.0, (Bonin et al. 2023)) AMRFinderPlus (version 3.11/2022-12-19.1, (Feldgarden et al. 2021)) ARGANNOT (V6_July2019, (Gupta et al. 2014)) The 'CsabaPal' collection (Provided by Csaba Pál and Zoltán Farkas in November 2022, Daruka et al. 2023)) BacMet (version 1.1, (Pal et al. 2014))