Table 5.

Element-based methods for identifying functional motifs

Local structure	Method	Software	Reference
Sequence motif
Binding sites	Multiple sequence alignment	–	Ma et al. (2003)
Catalytic sites	Multiple sequence alignment	Conservation	Capra and Singh (2007)
Structural motif
Functional active sites	Surface comparison	–	Rosen et al. (1998)
Recurring 3D motifs	Geometric hashing for structure alignment	–	Fischer et al. (1994)
Protein–protein interfaces	Comparison and querying	BID	Fischer et al. (2003)
Functional sites	All-vs-all comparison (from FSSP)	Phunctioner	Pazos and Sternberg (2004)
Constructed surface cavity	Pairwise alignment and querying	pvSOAR	Binkowski et al. (2003b)
Geometric and electrostatic surfaces	Pairwise alignment and querying	eF-site	Kinoshita and Nakamura (2003)
Surface chemical groups	Querying for similarity	SuMo	Jambon et al. (2003)
Binding pockets	Alignment all-vs-all and clustering	CavBase	Schmitt et al. (2002)
Binding sites and interface	Comparison for similarity	I2I-SiteEngine	Shulman-Peleg et al. (2005)
Documented motif
Annotated sites	Alignment all-vs.-all and querying	PINTS	Stark and Russell (2003a)
Ligand-binding sites	Alignment all-vs.-all and querying	SiteBase	Gold and Jackson (2006a)
Known sites, especially interfaces	Querying for similarity	PDBSiteScan	Ivanisenko et al. (2004)
Sequence map to spatial motif
Functional residues and sites	Multiple sequence alignment and phylogenetic	ET	Yao et al. (2003)
Functional residue clusters	Based on ET	–	Landgraf et al. (2001)
Patches of conserved residues	Based on ET	ConSurf	Armon et al. (2001)
Functional sites	Based on ET	–	Aloy et al. (2001)
Function template
Functional 3D templates	Matching by geometric hashing	TESS	Wallace et al. (1997)
Metal-binding sites	Comparison with templates	PAR-3D	Goyal and Mande (2007)
Annotated functional sites	Comparison with templates	FIC	Chakrabarti and Lanczycki (2007)
Tertiary side-chain patterns	Subgraph-isomorphism matching	ASSAM	Artymiuk et al. (1994)