Table 1.
Summary table.
| ArachnoServer | ConoServer | UniProtKB/Swiss-Prot | ATDB (metadatabase) | |
|---|---|---|---|---|
| Topic | Spider toxins | Conotoxins | General interest, includes animal toxins and their targets | Animal toxins and their targets |
| Sequences | Mature peptides and precursors | Mature peptides and precursors | Longest available protein sequences (precursors or mature sequences) (nucleotide sequences available via cross-references to EMBL/GenBank/DDBJ) | Protein sequences (as in source database), and some nucleotide sequences |
| Nucleotide sequences | Nucleotide sequences | |||
| Tools | BLAST | Sequence search, Fingerprint Search | BLAST, ProtParam, Compute pI/MW, ProtScale | BLAST |
| Clustal alignment, Digest Peptide, Analyse prosequence | PeptideMass, PeptideCutter | |||
| Cross-references | EMBL, UniProtKB | GenBank, GenPept, UniProtKB | EMBL/GenBank/DDBJ | GenBank, GenPept, UniProtKB, SCORPION2 (obsolete) |
| ArachnoServer | Snake neurotoxin database (obsolete) | |||
| ConoServer (work-in-process) | MOLLUSK (obsolete) | |||
| Sequence download | In FASTA format | In FASTA format | In FASTA format | In FASTA format |
| PTMs | Experimental PTMs (direct and indirect evidences indicated) | Experimental PTMs (disulfide bonds only indicated in cysteine framework) | Experimental PTMs (direct and indirect evidences indicated) | As in source database. |
| Search | Via the search tool or the browser | Only disulfide bonds (via the cysteine framework) | Via the search tool | Only disulfide bonds |
| 3D-structure | Shown if available | Shown if available | Available via cross-references to PDBsum and SMR (3D modeling) | Shown if available |
| Cross-references | PDB | PDB | PDB | PDB |
| BMRB | PDBsum | |||
| SMR | ||||
| Functions and Targets | In ‘Description’ (free text) and ‘Biological Activity’ (controlled vocabulary) | In ‘Classification’, a Greek letter indicates the target | In ‘General annotation (free text) and ‘Ontologies’ (controlled vocabulary) | In ‘Description’ using ‘Toxin ontology’ terms (controlled vocabulary). |
| As in source database (free text) | ||||
| Toxin effectiveness | In ‘Biological activity’. | Not indicated | In ‘General annotation’ | As in source database |
| Animal testing (LD(50), ED(50), PD(50)) | In ‘Biological activity’. | Not indicated | In ‘General annotation’ | As in source database |
| Channel and receptor nomenclature | IUPHAR | Not indicated | IUPHAR | IUPHAR |
| HGNC (only for human proteins and propagated to mammalian orthologs) | HGNC(only for mammalian proteins and propagated to mammalian orthologs) | |||
| Enzymes | In ‘Description’ (free text) and ‘Biological Activity’. | none | In ‘General annotation’ | As in source database |
| (EC number in ‘Protein names’) | ||||
| Active site and Metal binding | Not indicated | In ‘Sequence annotation (Features)’ | As in source database | |
| Cross-references | MEROPS | MEROPS | ||
| BRENDA | ||||
| Nomenclature | Creation of new names and names from the literature | Names from the literature | Names from the literature | As in source database |