Web-based Computational Tools Used in Protein Surface Analysis and Characterization. Applications for Protein–Protein and Protein–Ligand Interactions - Exotic Properties of Carbon Nanomatter - page 218

Fig. 9.14 Two WW structural
motifs of the human WW
domain binding protein 4,
PDB code entry 2JXW. The
four tryptophan residues (two
for each WW motif) are
shown in full and colored in
red
Fig. 9.15 PDZ structural
motifs of the human multiple
PDZ domain protein, PDB
code entry 2IWO
Several computational prediction methods exploit the conservation of protein-
binding interfaces by identifying domain pairs that constantly co-occur in interacting
proteins and use them to predict new interactions (Deng et al. 2002 ;Ngetal. 2003 ;
Guimaraes et val. 2006 ; Betel et al. 2007 ). There is a library of 3-D structures of pro-
tein complexes containing a detailed description of the binding interfaces between
interacting proteins (Salama et al. 2001 ). Such a library is used by structure-based
prediction methods to model interactions between proteins that are homologous in
structure to the complex components (Aloy et al. 2004 ; Hou et al. 2006 ). Other
prediction methods use integrative approaches incorporating experimentally proved
interaction and additional functional information: correlated expression level, com-
mon functional annotation, cross-species comparisons (Li et al. 2004 ; Betel et al.
2007 ).