Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding

Slavov, Svetoslav H; Pearce, Bruce A; Buzatu, Dan A; Wilkes, Jon G; Beger, Richard D

doi:10.1186/1758-2946-5-47

Journal of Cheminformatics

Table 3 Average statistical parameters of the best PLS and KNN models at a given number of LVs and neighbors as a function of the granularity of the 3D-SDAR space

From: Complementary PLS and KNN algorithms for improved 3D-QSDAR consensus modeling of AhR binding

Bin size	Optimal number of LVs	Avg. R²test (PLS)	Std. R²test (PLS)	Avg. R²scr (PLS)	Std. R²scr (PLS)	Optimal number of neighbors	Avg. R²test (KNN)	Std. R²test (KNN)
2 ppm x 2 ppm x 0.5 Å	3	0.591	0.143	0.085	0.103	6	0.618*	0.170
4 ppm x 4 ppm x 0.5 Å	3	0.604	0.142	0.088	0.109	5	0.606	0.146
6 ppm x 6 ppm x 0.5 Å	5	0.532	0.167	0.074	0.097	7	0.453	0.178
8 ppm x 8 ppm x 0.5 Å	5	0.593	0.142	0.097	0.113	6	0.520	0.162
10 ppm x 10 ppm x 0.5 Å	7	0.633*	0.147	0.085	0.113	4	0.612	0.162
12 ppm x 12 ppm x 0.5 Å	3	0.474	0.178	0.105	0.115	9	0.432	0.181
14 ppm x 14 ppm x 0.5 Å	2	0.321	0.193	0.096	0.121	10	0.312	0.179
16 ppm x 16 ppm x 0.5 Å	3	0.383	0.154	0.073	0.090	10	0.353	0.166
18 ppm x 18 ppm x 0.5 Å	2	0.307	0.189	0.077	0.100	10	0.307	0.186
20 ppm x 20 ppm x 0.5 Å	2	0.410	0.178	0.122	0.137	9	0.356	0.180
2 ppm x 2 ppm x 1.0 Å	3	0.567	0.149	0.082	0.095	6	0.599	0.181
4 ppm x 4 ppm x 1.0 Å	3	0.562	0.149	0.081	0.099	3	0.558	0.179
6 ppm x 6 ppm x 1.0 Å	5	0.526	0.164	0.076	0.099	7	0.466	0.178
8 ppm x 8 ppm x 1.0 Å	4	0.542	0.161	0.095	0.116	6	0.504	0.164
10 ppm x 10 ppm x 1.0 Å	6	0.597	0.153	0.086	0.100	4	0.593	0.162
12 ppm x 12 ppm x 1.0 Å	2	0.440	0.176	0.101	0.128	10	0.429	0.182
14 ppm x 14 ppm x 1.0 Å	2	0.315	0.195	0.100	0.125	10	0.327	0.179
16 ppm x 16 ppm x 1.0 Å	5	0.251	0.147	0.069	0.090	10	0.357	0.168
18 ppm x 18 ppm x 1.0 Å	2	0.296	0.189	0.077	0.106	10	0.292	0.185
20 ppm x 20 ppm x 1.0 Å	2	0.405	0.176	0.128	0.137	10	0.358	0.180
2 ppm x 2 ppm x 1.5 Å	3	0.537	0.163	0.074	0.087	5	0.603	0.178
4 ppm x 4 ppm x 1.5 Å	3	0.542	0.151	0.077	0.101	6	0.574	0.160
6 ppm x 6 ppm x 1.5 Å	5	0.536	0.164	0.073	0.112	5	0.481	0.169
8 ppm x 8 ppm x 1.5 Å	8	0.500	0.196	0.090	0.106	9	0.498	0.164
10 ppm x 10 ppm x 1.5 Å	8	0.531	0.180	0.092	0.106	5	0.585	0.166
12 ppm x 12 ppm x 1.5 Å	2	0.440	0.174	0.104	0.132	10	0.421	0.180
14 ppm x 14 ppm x 1.5 Å	8	0.267	0.155	0.073	0.082	10	0.316	0.181
16 ppm x 16 ppm x 1.5 Å	6	0.286	0.147	0.063	0.081	10	0.359	0.169
18 ppm x 18 ppm x 1.5 Å	2	0.302	0.188	0.079	0.111	7	0.291	0.180
20 ppm x 20 ppm x 1.5 Å	2	0.406	0.176	0.121	0.138	10	0.365	0.182
2 ppm x 2 ppm x 2.0 Å	2	0.495	0.177	0.071	0.086	6	0.576	0.180
4 ppm x 4 ppm x 2.0 Å	3	0.504	0.158	0.080	0.102	7	0.535	0.172
6 ppm x 6 ppm x 2.0 Å	5	0.500	0.170	0.071	0.095	6	0.467	0.173
8 ppm x 8 ppm x 2.0 Å	4	0.508	0.159	0.095	0.121	10	0.481	0.169
10 ppm x 10 ppm x 2.0 Å	4	0.498	0.174	0.088	0.105	10	0.557	0.174
12 ppm x 12 ppm x 2.0 Å	3	0.450	0.171	0.102	0.116	10	0.430	0.181
14 ppm x 14 ppm x 2.0 Å	9	0.297	0.156	0.078	0.093	10	0.329	0.186
16 ppm x 16 ppm x 2.0 Å	7	0.207	0.142	0.057	0.075	10	0.359	0.166
18 ppm x 18 ppm x 2.0 Å	2	0.273	0.179	0.070	0.112	10	0.308	0.188
20 ppm x 20 ppm x 2.0 Å	2	0.410	0.174	0.131	0.137	10	0.383	0.179
2 ppm x 2 ppm x 2.5 Å	2	0.481	0.18	0.076	0.087	8	0.555	0.185
4 ppm x 4 ppm x 2.5 Å	3	0.485	0.163	0.079	0.101	7	0.522	0.182
6 ppm x 6 ppm x 2.5 Å	5	0.492	0.165	0.071	0.101	7	0.465	0.175
8 ppm x 8 ppm x 2.5 Å	3	0.422	0.173	0.097	0.122	6	0.485	0.175
10 ppm x 10 ppm x 2.5 Å	10	0.471	0.222	0.072	0.082	3	0.568	0.172
12 ppm x 12 ppm x 2.5 Å	2	0.404	0.174	0.097	0.135	10	0.429	0.180
14 ppm x 14 ppm x 2.5 Å	8	0.286	0.158	0.073	0.094	10	0.315	0.186
16 ppm x 16 ppm x 2.5 Å	7	0.244	0.133	0.057	0.076	10	0.339	0.167
18 ppm x 18 ppm x 2.5 Å	3	0.282	0.173	0.081	0.092	10	0.293	0.184
20 ppm x 20 ppm x 2.5 Å	1	0.397	0.176	0.137	0.152	10	0.358	0.176

*indicates the best PLS and KNN models.

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ISSN: 1758-2946

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