Table 7.
Network-based methods for identifying functional motifs
| Local structure | Method | Software | Reference |
|---|---|---|---|
| Micro level: mining the special residues or subgraphs in the structure graphs | |||
| Active site residues | High closeness value of residue interaction graphs | RIG | Amitai et al. (2004) |
| Functional residues | Residues of special topology in small-world network | – | del Sol et al. (2006) |
| Recurring side-chain patterns | Searching for similar subgraph | DRESPAT | Wangikar et al. (2003) |
| Structure motifs | Mining for cliques of the structure graph | CliqueHashing | Huan et al. (2006) |
| Macro level: similar groups of local structures | |||
| Functional pockets | Similar pocket groups | PSN | Liu et al. (2007b) |