Fold classification based on secondary structure – how much is gained by including loop topology?

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa

doi:10.1186/1472-6807-6-3

BMC Structural Biology

Table 2 Raw scores and log-odds scores for individual folds.

From: Fold classification based on secondary structure – how much is gained by including loop topology?

fold number	fold size	score			Log-odds score			impact on the average
			ours			ours
		SSEA	NCL	CL	SSEA	NCL	CL	U	R	L
1	242	0.462	0.461	0.493	0.748	0.751	0.813			2
2	27	0.054	0.089	0.077	0.293	0.832	0.659
3	11	0.096	0.087	0.096	1.276	1.238	1.274
4	2	1.000	1.000	1.000	3.952	4.030	3.945
6	40	0.199	0.303	0.257	1.366	1.815	1.619		-1	-1
7	15	0.299	0.378	0.315	2.300	2.583	2.345
8	3	0.333	0.334	0.334	2.811	2.888	2.804
11	9	0.112	0.221	0.377	1.494	2.238	2.706	1	1
12	4	0.505	0.334	0.151	3.186	2.843	1.975	-2	-1
15	3	0.062	0.378	1.000	1.137	3.010	3.903	2	1
17	3	0.521	0.833	0.833	3.257	3.802	3.720
18	29	0.140	0.126	0.169	1.215	1.142	1.399		1	1
19	6	0.152	0.167	0.177	1.907	2.069	2.056
21	3	0.339	0.333	0.333	2.827	2.886	2.804
22	7	1.000	0.717	0.719	3.756	3.487	3.420
23	6	0.304	0.276	0.677	2.601	2.571	3.396	2	1
24	5	0.183	0.473	0.850	2.131	3.149	3.661	1
26	5	0.104	0.104	0.150	1.569	1.633	1.929
29	33	0.361	0.258	0.581	2.084	1.779	2.557	1	3	4
30	17	0.286	0.299	0.456	2.200	2.292	2.663		1	1
31	2	0.035	0.016	0.009	0.604	0.000	0.000
33	7	0.404	0.303	0.839	2.850	2.627	3.574	2	2	1
34	63	0.340	0.160	0.271	1.582	0.846	1.354	1	3	5
35	3	0.104	0.043	0.021	1.648	0.837	0.063	-1	-1
36	20	0.638	0.492	0.680	2.927	2.709	2.986		1
37	2	0.008	0.004	0.000	0.000	0.000	0.000
38	11	0.610	0.228	0.418	3.129	2.201	2.745	1	1	1
39	2	1.000	1.000	1.000	3.952	4.030	3.945
40	90	0.244	0.277	0.301	0.973	1.112	1.182			1
41	2	1.000	1.000	1.000	3.952	4.030	3.945
42	24	0.389	0.309	0.447	2.340	2.149	2.475		1	1
43	27	0.300	0.244	0.246	2.016	1.844	1.813
44	3	0.833	0.418	0.333	3.727	3.112	2.804
45	4	0.376	1.000	1.000	2.890	3.941	3.862
46	2	0.001	0.039	0.000	0.000	0.787	0.000	-1
47	32	0.753	0.424	0.395	2.838	2.296	2.189
49	2	1.000	1.000	1.000	3.952	4.030	3.945
50	11	0.382	0.352	0.331	2.662	2.635	2.513
51	4	0.199	0.502	0.531	2.254	3.251	3.230
52	10	0.353	0.256	0.308	2.615	2.351	2.471
53	3	0.003	0.064	0.500	0.000	1.235	3.210	4	2	1
55	30	0.531	0.492	0.607	2.526	2.483	2.656
56	2	1.000	1.000	1.000	3.952	4.030	3.945
57	3	1.000	1.000	1.000	3.910	3.984	3.903
58	3	0.335	1.000	1.000	2.815	3.984	3.903
60	22	0.489	0.488	0.478	2.613	2.652	2.587
61	9	0.127	0.084	0.352	1.623	1.264	2.637	3	3	2
62	2	1.000	1.000	1.000	3.952	4.030	3.945
63	2	1.000	1.000	1.000	3.952	4.030	3.945
64	2	0.016	1.000	1.000	0.000	4.030	3.945
65	2	0.126	0.001	0.063	1.877	0.000	1.174	2	1
66	5	1.000	0.900	1.000	3.830	3.793	3.824
67	2	0.002	0.016	0.000	0.000	0.000	0.000
68	13	0.550	0.382	0.552	2.966	2.653	2.964
69	23	0.747	0.711	0.750	3.014	3.005	3.015
70	5	0.475	0.368	0.591	3.086	2.900	3.297
71	24	0.342	0.148	0.281	2.212	1.412	2.010	1	2	2
72	10	0.602	0.454	0.533	3.148	2.922	3.021
74	4	1.000	1.000	1.000	3.869	3.941	3.862
76	2	0.000	0.531	0.000	0.000	3.397	0.000	-8	-3	-1
77	5	0.331	0.259	0.303	2.725	2.549	2.629
80	18	0.302	0.305	0.431	2.228	2.282	2.582		1
81	9	0.559	0.643	0.591	3.106	3.304	3.156
82	35	0.173	0.205	0.399	1.311	1.512	2.143	1	3	3
83	2	0.258	0.031	0.012	2.597	0.565	0.000	-1
84	14	0.165	0.143	0.225	1.735	1.638	2.038		1
85	14	0.076	0.070	0.141	0.959	0.924	1.571	1	1	1
86	3	0.355	1.000	1.000	2.874	3.984	3.903
87	4	0.167	0.208	0.501	2.080	2.373	3.171	1	1
88	3	0.089	0.011	0.048	1.489	0.000	0.870	2	1
91	2	0.750	1.000	1.000	3.664	4.030	3.945
92	2	0.009	0.008	0.062	0.000	0.000	1.172	2	1
93	2	1.000	1.000	1.000	3.952	4.030	3.945
104	2	0.094	0.125	0.500	1.585	1.951	3.252	3	1
106	3	0.006	0.009	0.003	0.000	0.000	0.000
108	2	0.250	0.002	0.000	2.566	0.000	0.000
113	4	1.000	0.875	1.000	3.869	3.807	3.862
118	2	1.000	1.000	1.000	3.952	4.030	3.945
121	49	0.211	0.246	0.305	1.287	1.465	1.654		1	1
122	5	0.157	0.120	0.188	1.978	1.779	2.153
125	2	1.000	1.000	1.000	3.952	4.030	3.945
Unweighted avg.		0.417	0.434	0.501	2.300	2.368	2.500
$\sqrt{s i z e}$ weighted avg.		0.389	0.378	0.453	2.080	2.088	2.263
weighted avg.		0.376	0.351	0.421	1.705	1.675	1.853

Raw scores and log-odds scores for 81 folds that had more than one representative in our data. SSEA score was obtained by taking structure determinations of DSSP and computing the scores using the publically available binary code of SSEA program. Our scores were computed using our alignment program and using our structure determinations, which were similar but not identical to DSSP. Averages are: unweighted (U), root weighted (R) – fold with k proteins get weight $\sqrt{k}$ and weighted (L), where the weight is k. "Impact on the average" shows how the respective average would change if all other folds had identical scores; we multiply this change by 200 and round toward 0; zeroes are not shown.

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ISSN: 1472-6807

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