| InterPro | Database for the classification of proteins into families, domains and conserved sites |
| ConSurf-DB | Evolutionary conservation profiles of protein structures |
| OrthoDB | Hierarchical catalog of orthologs that can be searched using protein sequence, gene name, copy number and other identifiers |
| CDD | NCBI Conserved Domain Database |
| PANTHER | Protein ANalysis THrough Evolutionary Relationship |
| ProtCID | Protein Common Interfaces Database |
| SMART | SMART specializes in mobile protein domains involved in signaling, extracellular, and regulatory functions |
| TreeFam | Tree families database of phylogenetic trees of animal genes |
