The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

Table 3 Results of NMR ensembles scanned with FEATURE Ca²⁺ binding site model

Protein Name	PDB ID	Number of Models	Number of Models Characterized as Calcium Binding
Lipoprotein receptor-related protein repeat 8	1CR8	20	20
Lipoprotein receptor-related protein repeat 3	1D2L	20	20
RALBP1-intercating protein	1IQ3	18	18
Rous Sarcoma virus receptor	1JRF	20	20
Tyrosine-protein kinase SRC	1KSW	20	20
Calerythrin	1NYA	20	20
Human Notch1	1PB5	16	16
Porcine pancreas phospholipase A2	1SFW	18	1
Rational design of a calcium-binding adhesion protein	1T6W	20	3
Human beta parvalbumin	1TTX	20	20
Cytochrome c peroxidase *	2B10	10	4
Matrilysin	2DDY	25	24
Calcium-binding protein p22	2E+30	20	17
Sodium/calcium exchanger 1 domain 1	2FWS	20	18
Sodium/calcium exchanger 1 domain 2	2FWU	20	18
Rat megalin	2I1P	20	19
Relaxin receptor 1	2JM4	24	22
Yeast frequenin	2JU0	15	15

Scanning of the 18 NMR ensembles with the Ca²⁺ binding model revealed structural heterogeneity among the structures in the ensembles. In several, most of the models exhibited Ca²⁺ binding conformations, while in others, only a few. The first and the second columns contain names and PDB IDs of the examined proteins, respectively. The third and fourth columns show the total number of models and how many of those were identified by FEATURE as Ca²⁺ binding in the NMR ensemble, respectively. * – Results of this scan are shown in Figure 4.

ISSN: 1471-2164