. 2018 Oct 16;5:180212. doi: 10.1038/sdata.2018.212

Table 1. Distribution of the 429 active resources in the NAR Molecular Biology Database Collection that utilize PDB archive data across major categories (bold) and subcategory (italics), and corresponding resources in the “golden set”⁴¹ of the NAR Molecular Biology Database Collection.

NAR Category and Subcategory	Number that Utilize PDB Data	NAR Golden Set
wwPDB partners RCSB PDB, PDBe, and PDBj are included in the subcategory Protein Structure.
Structure Databases	107
Protein Structure	81	MMDB⁴⁷, PDBe,⁶ PDBsum⁴⁸, RCSB PDB,^5,10 SCOP2⁴⁹, SUPERFAMILY⁵⁰, SWISS-MODEL Repository⁵¹
Small Molecules	11	ChEBI⁵², PubChem⁵³
Nucleic Acid Structure	8
Carbohydrates	7
Protein Sequence Databases	95
Databases of Individual Protein Families	42	GPCRDB⁵⁴, MEROPS⁵⁵
Protein Domain Databases; Protein Classification	14	CDD⁵⁶, CATH⁵⁷, Pfam⁵⁸, SMART⁵⁹
Protein Sequence Motifs and Active Sites	15	ELM⁶⁰, PROSITE⁶¹
Protein Properties	10	dbPTM⁶²
Protein Localization and Targeting	8
General Sequence Databases	6	PIR⁶³, TCDB⁶⁴, UniProt⁶⁵
Metabolic and Signaling Pathways	58
Protein-Protein Interactions	30	STITCH⁶⁶, STRING⁶⁷
Enzymes and Enzyme Nomenclature	14	CAZy⁶⁸
Metabolic Pathways	10	BioCyc⁶⁹, HMDB⁷⁰, MODOMICS⁷¹, Reactome⁷²
Signaling Pathways	4
Genomics Databases (Non-Vertebrate)	47
Prokaryotic Genome Databases	11	EcoCyc⁷³
Viral Genome Databases	9
Unicellular Eukaryotes Genome Databases	8
Invertebrate Genome Databases	7	VectorBase⁷⁴
Fungal Genome Databases	6	CGD⁷⁵, SGD⁷⁶
Genome Annotation Terms, Ontologies, and Nomenclature	4	Genenames⁷⁷
General Genomics Databases	2	KEGG⁷⁸, MetaCyc⁶⁹
Human Genes and Diseases	23
General Polymorphism Databases	5
General Human Genetics Databases	3
Gene-, System- or Disease-Specific Databases	7
Cancer Gene Databases	7	CanSAR⁷⁹
Human Genes and Diseases	1	COSMIC⁸⁰
Other Molecular Biology Databases	25
Drugs and Drug Design	21	ChEMBL⁸¹
No Subcategory	3
Molecular Probes and Primers	1
Nucleotide Sequence Databases	20
Transcriptional Regulator Sites and Transcription Factors	11	JASPAR⁸²
Gene Structure, Introns and Exons, Splice Sites	5
International Nucleotide Sequence Database Collaboration	3	DDBJ⁸³, ENA⁸⁴
Coding and Non-Coding DNA	1
Immunological Databases	12	IEDB⁸⁵, IMGT⁸⁶
RNA Sequence Databases	12	NONCODE⁸⁷, Rfam⁸⁸
Human and Other Vertebrate Genomes	11
Human ORFs	5	FANTOM⁸⁹, neXtProt⁹⁰
Model Organisms, Comparative Genomics	4	Ensembl⁹¹, Mouse Genome Database⁹², Rat Genome Database⁹³
Human Genome Databases, Maps and Viewers	2	UCSC Genome Browser⁹⁴
Plant Databases	7
General Plant Databases	5
Arabidopsis thaliana	1
Other Plants	1
Proteomics Resources	8	dbPTM⁶²
Microarray Data and Other Gene Expression Databases	2	ArrayExpress⁹⁵
Organelle Databases	2

Table 1. Distribution of the 429 active resources in the NAR Molecular Biology Database Collection that utilize PDB archive data across major categories (bold) and subcategory (italics), and corresponding resources in the “golden set”41 of the NAR Molecular Biology Database Collection.

Table 1. Distribution of the 429 active resources in the NAR Molecular Biology Database Collection that utilize PDB archive data across major categories (bold) and subcategory (italics), and corresponding resources in the “golden set”⁴¹ of the NAR Molecular Biology Database Collection.