Relating the shape of protein binding sites to binding affinity profiles: is there an association?

BMC Structural Biology

Table 3 Explained variances of PCA Factors obtained from the PocketPicker descriptor matrix

Factor Number	Explained Variance	Cumulative Explained Variance
1	0.3847	0.3847
2	0.2359	0.6206
3	0.0818	0.7024
4	0.0544	0.7568
5	0.0524	0.8091
6	0.0377	0.8469
7	0.0257	0.8726
8	0.0180	0.8906
9	0.0136	0.9042
10	0.0120	0.9162
11	0.0100	0.9262
12	0.0078	0.9340
13	0.0074	0.9414
14	0.0057	0.9471
15	0.0049	0.9520
16	0.0041	0.9561
17	0.0038	0.9599
18	0.0029	0.9628
19	0.0029	0.9657
20	0.0028	0.9685
21	0.0025	0.9709
22	0.0022	0.9732
23	0.002	0.9752
24	0.0019	0.9771
25	0.0017	0.9788
26	0.0016	0.9804
27	0.0015	0.9819
28	0.0012	0.9831
29	0.0012	0.9843
30	0.0011	0.9854
31	0.0009	0.9863
32	0.0009	0.9872
33	0.0008	0.9880
34	0.0007	0.9888
35	0.0007	0.9895
36	0.0006	0.9901
37	0.0006	0.9908
38	0.0006	0.9913
39	0.0005	0.9919
40	0.0005	0.9924

The first 40 factors obtained from the factor analysis of the geometric features of the binding sites of 154 target proteins are shown. 13 factors were retained in accordance with the average variance criterion (i.e., explaining > 1/154 = 0.65% of the total variance). Cumulatively, they explain 94.1% of the total variance.

ISSN: 1472-6807