Hierarchical representation for PPI sites prediction

Quadrini, Michela; Daberdaku, Sebastian; Ferrari, Carlo

doi:10.1186/s12859-022-04624-y

BMC Bioinformatics

Table 4 Measures of F1 score, classification accuracy, precision, recall, MCC and ROC-AUC obtained on the test set of the receptors classes

From: Hierarchical representation for PPI sites prediction

	A class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.328	0.345	0.851	0.857	0.243	0.265	0.534	0.548	0.287	0.306	0.845	0.835
Contact Map 6 Å	0.622	0.629	0.947	0.930	0.631	0.526	0.665	0.864	0.608	0.631	0.975	0.980
Contact Map 8 Å	0.630	0.620	0.950	0.925	0.658	0.502	0.660	0.889	0.620	0.624	0.974	0.978
Contact Map 10 Å	0.578	0.628	0.920	0.940	0.467	0.602	0.823	0.724	0.576	0.617	0.970	0.975
Contact Map 12 Å	0.552	0.580	0.932	0.920	0.523	0.483	0.645	0.801	0.535	0.574	0.966	0.967
Hierarchical Representation 6Å	0.657	0.592	0.952	0.910	0.667	0.447	0.701	0.951	0.647	0.609	0.971	0.978
Hierarchical Representation 8Å	0.647	0.665	0.950	0.945	0.663	0.608	0.690	0.803	0.637	0.659	0.976	0.980
Hierarchical Representation 10Å	0.619	0.632	0.952	0.927	0.718	0.510	0.595	0.907	0.615	0.638	0.975	0.978
Hierarchical Representation 12Å	0.619	0.604	0.948	0.918	0.656	0.474	0.647	0.910	0.611	0.612	0.975	0.977
Other methods
Daberdaku et. al.	0.272	0.274	0.862	0.876	0.166	0.169	0.917	0.883	0.346	0.341	0.954	0.939
SPPIDER											0.773	0.754
NPS-HomPPI											0.796	0.780
PrISE											0.770	0.758

	AB class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.212	0.244	0.886	0.750	0.265	0.167	0.214	0.537	0.168	0.188	0.727	0.737
Contact Map 6 Å	0.432	0.400	0.930	0.930	0.535	0.391	0.425	0.443	0.422	0.382	0.942	0.939
Contact Map 8 Å	0.300	0.316	0.929	0.931	0.496	0.466	0.276	0.297	0.323	0.327	0.945	0.955
Contact Map 10 Å	0.406	0.293	0.924	0.926	0.589	0.304	0.391	0.302	0.424	0.291	0.958	0.965
Contact Map 12 Å	0.357	0.359	0.909	0.914	0.488	0.317	0.455	0.454	0.370	0.353	0.956	0.964
Hierarchical Representation 6Å	0.428	0.347	0.921	0.913	0.501	0.383	0.446	0.423	0.411	0.332	0.886	0.886
Hierarchical Representation 8Å	0.450	0.407	0.921	0.925	0.491	0.566	0.492	0.484	0.431	0.417	0.918	0.928
Hierarchical Representation 10Å	0.412	0.415	0.930	0.931	0.601	0.615	0.424	0.473	0.417	0.429	0.948	0.953
Hierarchical Representation 12Å	0.281	0.340	0.923	0.929	0.439	0.469	0.264	0.341	0.292	0.348	0.955	0.963
Other methods
Daberdaku et. al.	0.230	0.228	0.910	0.913	0.161	0.156	0.590	0.546	0.256	0.250	0.890	0.845
SPPIDER											0.757	0.783
NPS-HomPPI											0.701	0.698
PrISE											0.776	0.789

	EI class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.281	0.292	0.590	0.646	0.190	0.224	0.596	0.505	0.125	0.133	0.631	0.622
Contact Map 6 Å	0.303	0.349	0.827	0.713	0.344	0.275	0.326	0.610	0.231	0.262	0.753	0.732
Contact Map 8 Å	0.364	0.363	0.725	0.722	0.283	0.280	0.604	0.594	0.270	0.271	0.753	0.729
Contact Map 10 Å	0.327	0.378	0.734	0.720	0.299	0.310	0.521	0.580	0.233	0.281	0.755	0.708
Contact Map 12 Å	0.270	0.330	0.733	0.605	0.235	0.232	0.440	0.643	0.167	0.189	0.732	0.678
Hierarchical Representation 6Å	0.329	0.342	0.817	0.744	0.320	0.289	0.369	0.507	0.237	0.236	0.749	0.725
Hierarchical Representation 8Å	0.354	0.364	0.797	0.776	0.331	0.331	0.446	0.511	0.267	0.285	0.766	0.732
Hierarchical Representation 10Å	0.363	0.380	0.806	0.753	0.388	0.338	0.445	0.574	0.290	0.304	0.770	0.745
Hierarchical Representation 12Å	0.414	0.362	0.760	0.668	0.348	0.275	0.611	0.681	0.324	0.278	0.783	0.732
Other methods
Daberdaku et. al.	0.156	0.148	0.604	0.645	0.089	0.087	0.770	0.705	0.158	0.146	0.764	0.747
SPPIDER											0.696	0.673
NPS-HomPPI											0.720	0.682
PrISE											0.755	0.700

	ER class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.207	0.187	0.588	0.193	0.133	0.107	0.550	0.966	0.076	0.049	0.608	0.572
Contact Map 6 Å	0.186	0.211	0.106	0.691	0.106	0.157	1.000	0.480	0.000	0.115	0.635	0.663
Contact Map 8 Å	0.186	0.158	0.106	0.808	0.106	0.173	1.000	0.239	0.000	0.090	0.638	0.648
Contact Map 10 Å	0.186	0.179	0.106	0.103	0.106	0.102	1.000	1.000	0.000	0.000	0.655	0.634
Contact Map 12 Å	0.186	0.179	0.106	0.101	0.106	0.101	1.000	1.000	0.000	0.000	0.693	0.614
Hierarchical Representation 6Å	0.202	0.184	0.326	0.151	0.117	0.105	0.854	0.988	0.048	0.041	0.626	0.654
Hierarchical Representation 8Å	0.186	0.194	0.106	0.329	0.106	0.114	1.000	0.841	0.000	0.059	0.615	0.671
Hierarchical Representation 10Å	0.186	0.195	0.106	0.245	0.106	0.112	1.000	0.929	0.000	0.039	0.590	0.654
Hierarchical Representation 12Å	0.186	0.173	0.106	0.675	0.106	0.151	1.000	0.408	0.000	0.054	0.596	0.655
Other methods
Daberdaku et. al.	0.145	0.109	0.733	0.747	0.089	0.065	0.580	0.465	0.136	0.092	0.734	0.663
SPPIDER											0.731	0.736
NPS-HomPPI											0.588	0.589
PrISE											0.742	0.674

	ES class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.257	0.232	0.512	0.278	0.163	0.137	0.663	0.879	0.097	0.070	0.596	0.565
Contact Map 6 Å	0.228	0.247	0.693	0.617	0.180	0.167	0.351	0.542	0.070	0.111	0.608	0.608
Contact Map 8 Å	0.241	0.302	0.586	0.623	0.176	0.210	0.534	0.627	0.097	0.186	0.612	0.645
Contact Map 10 Å	0.255	0.292	0.621	0.601	0.215	0.201	0.524	0.672	0.131	0.192	0.621	0.660
Contact Map 12 Å	0.263	0.239	0.642	0.326	0.211	0.143	0.511	0.829	0.140	0.064	0.626	0.658
Hierarchical Representation 6Å	0.204	0.248	0.748	0.478	0.187	0.155	0.248	0.689	0.064	0.102	0.607	0.580
Hierarchical Representation 8Å	0.236	0.261	0.678	0.663	0.185	0.184	0.388	0.511	0.080	0.135	0.621	0.604
Hierarchical Representation 10Å	0.245	0.284	0.673	0.545	0.192	0.181	0.416	0.752	0.094	0.185	0.620	0.631
Hierarchical Representation 12Å	0.230	0.272	0.717	0.436	0.229	0.167	0.353	0.825	0.114	0.154	0.625	0.651
Other methods
Daberdaku et. al.	0.031	0.121	0.954	0.861	0.086	0.090	0.023	0.281	0.023	0.096	0.712	0.709
SPPIDER											0.742	0.727
NPS-HomPPI											0.604	0.654
PrISE											0.742	0.664

	OG class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.276	0.248	0.721	0.603	0.222	0.178	0.384	0.491	0.122	0.072	0.596	0.572
Contact Map 6 Å	0.389	0.288	0.755	0.806	0.298	0.295	0.617	0.313	0.285	0.196	0.756	0.711
Contact Map 8 Å	0.305	0.274	0.580	0.532	0.210	0.176	0.705	0.735	0.163	0.157	0.728	0.730
Contact Map 10 Å	0.300	0.259	0.685	0.603	0.252	0.199	0.444	0.580	0.128	0.129	0.682	0.735
Contact Map 12 Å	0.266	0.190	0.431	0.602	0.168	0.126	0.735	0.515	0.059	0.083	0.688	0.704
Hierarchical Representation 6Å	0.359	0.244	0.744	0.772	0.281	0.230	0.550	0.324	0.240	0.140	0.717	0.662
Hierarchical Representation 8Å	0.355	0.292	0.706	0.794	0.253	0.274	0.647	0.386	0.241	0.209	0.743	0.707
Hierarchical Representation 10Å	0.351	0.351	0.709	0.752	0.257	0.266	0.602	0.605	0.221	0.278	0.764	0.748
Hierarchical Representation 12Å	0.323	0.326	0.692	0.778	0.239	0.285	0.555	0.496	0.175	0.259	0.744	0.742
Other methods
Daberdaku et. al.	0.184	0.144	0.704	0.805	0.113	0.103	0.552	0.340	0.145	0.100	0.700	0.631
SPPIDER											0.748	0.753
NPS-HomPPI											0.699	0.768
PrISE											0.686	0.673

	OR class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.249	0.255	0.229	0.467	0.149	0.187	0.949	0.672	0.040	0.033	0.572	0.547
Contact Map 6 Å	0.191	0.201	0.582	0.540	0.138	0.179	0.407	0.424	-0.002	-0.009	0.577	0.507
Contact Map 8 Å	0.173	0.284	0.683	0.318	0.173	0.193	0.272	0.887	0.021	0.021	0.586	0.494
Contact Map 10 Å	0.207	0.287	0.604	0.315	0.162	0.195	0.440	0.891	0.042	0.017	0.600	0.502
Contact Map 12 Å	0.245	0.288	0.531	0.316	0.167	0.196	0.587	0.897	0.067	0.027	0.621	0.492
Hierarchical Representation 6Å	0.159	0.178	0.676	0.601	0.127	0.162	0.266	0.343	-0.009	-0.012	0.546	0.508
Hierarchical Representation 8Å	0.192	0.198	0.614	0.508	0.141	0.155	0.382	0.432	0.002	-0.077	0.566	0.499
Hierarchical Representation 10Å	0.172	0.211	0.659	0.569	0.146	0.169	0.303	0.400	0.002	-0.049	0.562	0.505
Representation 12Å	0.213	0.276	0.608	0.281	0.162	0.188	0.447	0.846	0.043	-0.031	0.584	0.492
Other methods
Daberdaku et. al.	0.121	0.103	0.662	0.115	0.073	0.057	0.558	0.968	0.093	0.024	0.659	0.626
SPPIDER											0.691	0.667
NPS-HomPPI											0.712	0.642
PrISE											0.655	0.642

	OX class—receptors
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.213	0.208	0.219	0.264	0.12459	0.120	0.939	0.901	0.051	0.055	0.583	0.594
Contact Map 6 Å	0.218	0.220	0.268	0.414	0.128	0.140	0.926	0.759	0.064	0.082	0.632	0.619
Contact Map 8 Å	0.226	0.198	0.345	0.437	0.137	0.169	0.858	0.710	0.091	0.073	0.643	0.630
Contact Map 10 Å	0.227	0.186	0.390	0.420	0.139	0.111	0.814	0.707	0.090	0.045	0.636	0.627
Contact Map 12 Å	0.227	0.181	0.440	0.443	0.141	0.108	0.752	0.654	0.089	0.033	0.622	0.619
Hierarchical Representation 6Å	0.216	0.201	0.249	0.167	0.126	0.115	0.928	0.965	0.056	0.025	0.614	0.601
Hierarchical Representation 8Å	0.218	0.215	0.272	0.328	0.128	0.127	0.921	0.854	0.063	0.066	0.620	0.604
Hierarchical Representation 10Å	0.219	0.209	0.272	0.425	0.128	0.137	0.913	0.706	0.058	0.050	0.612	0.606
Hierarchical Representation 12Å	0.215	0.187	0.280	0.499	0.126	0.164	0.880	0.572	0.043	0.042	0.603	0.605
Other methods
Daberdaku et. al.	0.108	0.081	0.677	0.670	0.063	0.045	0.555	0.490	0.089	0.056	0.665	0.614
SPPIDER											0.667	0.640
NPS-HomPPI											0.612	0.635
PrISE											0.641	0.592

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com