Hierarchical representation for PPI sites prediction

Quadrini, Michela; Daberdaku, Sebastian; Ferrari, Carlo

doi:10.1186/s12859-022-04624-y

BMC Bioinformatics

Table 3 Measures of F1 score, classification accuracy, precision, recall, MCC and ROC-AUC obtained on the test set of the ligands classes

From: Hierarchical representation for PPI sites prediction

	A class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
	b	u	b	u	b	u	b	u	b	u	b	u
HSS-PPI
Residue Sequence	0.208	0.271	0.731	0.480	0.180	0.170	0.261	0.749	0.054	0.118	0.588	0.613
Contact Map 6 Å	0.266	0.259	0.297	0.302	0.158	0.155	0.919	0.943	0.074	0.108	0.651	0.704
Contact Map 8 Å	0.254	0.238	0.201	0.180	0.149	0.140	0.981	0.979	0.027	0.019	0.649	0.713
Contact Map 10 Å	0.252	0.240	0.199	0.224	0.148	0.141	0.966	0.939	0.028	0.030	0.625	0.697
Contact Map 12 Å	0.259	0.252	0.299	0.289	0.154	0.151	0.848	0.883	0.036	0.060	0.589	0.664
Hierarchical Representation 6Å	0.282	0.264	0.445	0.344	0.174	0.159	0.806	0.918	0.127	0.117	0.635	0.661
Hierarchical Representation 8Å	0.272	0.243	0.340	0.192	0.163	0.143	0.896	0.975	0.099	0.028	0.633	0.670
Hierarchical Representation 10Å	0.272	0.243	0.380	0.204	0.164	0.143	0.839	0.978	0.091	0.038	0.624	0.685
Hierarchical Representation 12Å	0.267	0.237	0.340	0.161	0.160	0.139	0.850	0.983	0.060	0.003	0.611	0.684
Other methods
Daberdaku et. al.	0.093	0.097	0.811	0.059	0.067	0.052	0.182	0.987	0.019	-0.016	0.538	0.473
SPPIDER											0.630	0.575
NPS-HomPPI											0.610	0.626
PrISE											0.622	0.569

	AB class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
	b	u	b	u	b	u	b	u	b	u	b	u
HSS-PPI
Residue Sequence	0.295	u	0.668	u	0.270	u	0.359	u	0.092	u	0.593	u
Contact Map 6 Å	0.325	0.465	0.415	0.715	0.247	0.372	0.792	0.625	0.132	0.292	0.733	0.743
Contact Map 8 Å	0.421	0.496	0.767	0.669	0.333	0.373	0.584	0.746	0.311	0.316	0.760	0.782
Contact Map 10 Å	0.403	0.482	0.715	0.571	0.311	0.431	0.635	0.713	0.315	0.217	0.826	0.777
Contact Map 12 Å	0.416	0.519	0.663	0.550	0.317	0.388	0.673	0.911	0.247	0.286	0.826	0.786
Hierarchical Representation 6Å	0.348	0.447	0.294	0.689	0.221	0.352	0.975	0.651	0.105	0.269	0.723	0.698
Hierarchical Representation 8Å	0.278	0.493	0.395	0.700	0.194	0.375	0.762	0.725	0.083	0.329	0.728	0.737
Hierarchical Representation 10Å	0.263	0.286	0.410	0.800	0.169	0.501	0.750	0.213	0.066	0.218	0.761	0.743
Hierarchical Representation 12Å	0.262	0.274	0.411	0.789	0.167	0.383	0.750	0.214	0.080	0.175	0.769	0.752
Other methods
Daberdaku et. al.	0.183	0.115	0.653	0.246	0.112	0.063	0.553	0.931	0.110	0.071	0.655	0.667
SPPIDER											0.573	0.556
NPS-HomPPI											0.676	0.713
PrISE											0.683	0.649

	EI class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
	b	u	b	u	b	u	b	u	b	u	b	u
HSS-PPI
Residue Sequence	0.414	0.399	0.415	0.482	0.287	0.292	0.792	0.678	0.038	0.053	0.601	0.565
Contact Map 6 Å	0.405	0.406	0.511	0.557	0.317	0.349	0.730	0.675	0.124	0.121	0.715	0.644
Contact Map 8 Å	0.343	0.387	0.545	0.483	0.242	0.281	0.637	0.752	0.080	0.059	0.687	0.636
Contact Map 10 Å	0.429	0.399	0.343	0.403	0.285	0.274	0.931	0.830	0.025	0.020	0.616	0.575
Contact Map 12 Å	0.422	0.393	0.308	0.397	0.278	0.268	0.947	0.830	-0.001	0.016	0.594	0.592
Hierarchical Representation 6Å	0.420	0.417	0.608	0.422	0.337	0.287	0.634	0.826	0.174	0.027	0.688	0.592
Hierarchical Representation 8Å	0.393	0.394	0.621	0.540	0.310	0.305	0.597	0.682	0.168	0.092	0.696	0.616
Hierarchical Representation 10Å	0.364	0.375	0.625	0.595	0.284	0.337	0.557	0.612	0.137	0.127	0.694	0.626
Hierarchical Representation 12Å	0.343	0.358	0.501	0.588	0.233	0.318	0.683	0.585	0.044	0.109	0.686	0.624
Other methods
Daberdaku et. al.	0.253	0.203	0.535	0.360	0.154	0.118	0.793	0.865	0.167	0.086	0.725	0.673
SPPIDER											0.755	0.732
NPS-HomPPI											0.701	0.744
PrISE											0.719	0.678

	ER class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
	b	u	b	u	b	u	b	u	b	u	b	u
HSS-PPI
Residue Sequence	0.386	0.331	0.356	0.339	0.260	0.230	0.879	0.853	0.076	0.071	0.593	0.597
Contact Map 6 Å	0.364	0.281	0.357	0.392	0.243	0.230	0.829	0.639	0.033	- 0.018	0.529	0.518
Contact Map 8 Å	0.370	0.281	0.321	0.392	0.244	0.230	0.886	0.639	0.012	-0.018	0.510	0.518
Contact Map 10 Å	0.382	0.327	0.270	0.233	0.251	0.224	0.976	0.928	0.036	0.012	0.506	0.523
Contact Map 12 Å	0.334	0.283	0.335	0.242	0.257	0.219	0.841	0.856	0.036	0.005	0.530	0.558
Hierarchical Representation 6Å	0.391	0.295	0.468	0.482	0.278	0.272	0.762	0.635	0.085	0.078	0.585	0.577
Hierarchical Representation 8Å	0.369	0.303	0.436	0.399	0.254	0.266	0.769	0.724	0.075	0.079	0.556	0.560
Hierarchical Representation 10Å	0.347	0.268	0.452	0.430	0.240	0.255	0.724	0.589	0.054	0.005	0.532	0.526
Hierarchical Representation 12Å	0.345	0.237	0.438	0.410	0.242	0.238	0.730	0.544	0.030	-0.043	0.524	0.485
Other methods
Daberdaku et. al.	0.214	0.137	0.494	0.087	0.136	0.077	0.851	0.998	0.167	0.019	0.774	0.685
SPPIDER											0.778	0.740
NPS-HomPPI											0.643	0.761
PrISE											0.700	0.680

	ES class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
	b	u	b	u	b	u	b	u	b	u	b	u
HSS-PPI
Residue Sequence	0.301	0.309	0.533	0.379	0.214	0.199	0.568	0.797	0.069	0.059	0.578	0.552
Contact Map 6 Å	0.333	0.330	0.487	0.359	0.232	0.217	0.708	0.862	0.127	0.089	0.620	0.601
Contact Map 8 Å	0.318	0.315	0.222	0.219	0.198	0.196	0.995	0.995	0.061	0.059	0.611	0.607
Contact Map 10 Å	0.317	0.322	0.227	0.247	0.196	0.201	0.995	0.995	0.068	0.098	0.616	0.620
Contact Map 12 Å	0.302	0.331	0.189	0.272	0.182	0.207	1.000	0.994	0.025	0.107	0.620	0.639
Hierarchical Representation 6Å	0.320	0.323	0.523	0.534	0.227	0.237	0.633	0.615	0.102	0.114	0.602	0.591
Hierarchical Representation 8Å	0.305	0.305	0.482	0.482	0.221	0.221	0.636	0.636	0.093	0.093	0.590	0.590
Hierarchical Representation 10Å	0.323	0.310	0.359	0.270	0.222	0.200	0.824	0.914	0.103	0.040	0.597	0.573
Hierarchical Representation 12Å	0.314	0.323	0.279	0.233	0.202	0.204	0.914	0.995	0.079	0.074	0.617	0.587
Other methods
Daberdaku et. al.	0.150	0.169	0.665	0.636	0.087	0.102	0.665	0.670	0.142	0.148	0.703	0.720
SPPIDER											0.778	0.740
NPS-HomPPI											0.643	0.671
PrISE											0.700	0.680

	OG class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Sequence Å	0.285	0.249	0.641	0.699	0.206	0.232	0.486	0.278	0.114	0.055	0.605	0.552
Contact Map 6 Å	0.329	0.367	0.398	0.472	0.203	0.242	0.933	0.871	0.181	0.178	0.722	0.659
Contact Map 8 Å	0.317	0.329	0.352	0.540	0.196	0.261	0.935	0.730	0.140	0.150	0.703	0.684
Contact Map 10 Å	0.304	0.193	0.313	0.741	0.191	0.245	0.923	0.230	0.103	0.110	0.712	0.677
Contact Map 12 Å	0.211	0.299	0.669	0.555	0.184	0.203	0.420	0.656	0.106	0.092	0.659	0.677
Hierarchical Representation 6Å	0.360	0.397	0.567	0.551	0.241	0.270	0.786	0.837	0.230	0.229	0.749	0.684
Hierarchical Representation 8Å	0.352	0.381	0.455	0.491	0.224	0.258	0.918	0.871	0.227	0.194	0.758	0.683
Hierarchical Representation 10Å	0.335	0.072	0.403	0.775	0.215	0.086	0.922	0.065	0.185	0.001	0.744	0.678
Hierarchical Representation 12Å	0.312	0.207	0.345	0.750	0.194	0.280	0.929	0.226	0.137	0.098	0.721	0.684
Other methods
Daberdaku et. al.	0.127	0.108	0.373	0.089	0.069	0.058	0.927	0.996	0.125	0.037	0.622	0.653
SPPIDER											0.663	0.659
NPS-HomPPI											0.707	0.722
PrISE											0.693	0.658

	OR class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.398	0.387	0.410	0.547	0.282	0.335	0.873	0.611	0.128	0.107	0.598	0.591
Contact Map 6 Å	0.191	0.263	0.582	0.709	0.138	0.374	0.407	0.276	-0.002	0.175	0.577	0.656
Contact Map 8 Å	0.238	0.220	0.653	0.630	0.356	0.355	0.343	0.249	0.112	0.052	0.646	0.648
Contact Map 10 Å	0.221	0.435	0.627	0.349	0.220	0.317	0.360	0.986	0.053	0.045	0.671	0.594
Contact Map 12 Å	0.220	0.436	0.504	0.350	0.244	0.313	0.502	1.000	0.035	0.043	0.665	0.568
Hierarchical Representation 6Å	0.338	0.393	0.725	0.583	0.392	0.378	0.359	0.602	0.194	0.186	0.656	0.660
Hierarchical Representation 8Å	0.343	0.376	0.672	0.574	0.388	0.398	0.437	0.576	0.194	0.199	0.607	0.681
Hierarchical Representation 10Å	0.263	0.35	0.732	0.522	0.455	0.391	0.284	0.606	0.201	0.176	0.692	0.682
Hierarchical Representation 12Å	0.269	0.239	0.712	0.704	0.342	0.402	0.375	0.254	0.207	0.180	0.704	0.676
Other methods
Daberdaku et. al.	0.172	0.190	0.269	0.592	0.098	0.153	0.980	0.593	0.120	0.095	0.723	0.658
SPPIDER											0.698	0.613
NPS-HomPPI											0.681	0.691
PrISE											0.698	0.601

	OX class—ligands
	F1		Accuracy		Precision		Recall		MCC		AUC-ROC
HSS-PPI
Residue Sequence	0.347	0.360	0.310	0.242	0.218	0.230	0.935	0.986	0.059	0.007	0.565	0.536
Contact Map 6 Å	0.218	0.347	0.268	0.265	0.128	0.222	0.926	0.950	0.064	0.006	0.632	0.552
Contact Map 8 Å	0.335	0.356	0.207	0.249	0.207	0.228	1.000	0.968	0.000	-0.002	0.553	0.537
Contact Map 10 Å	0.335	0.361	0.207	0.246	0.207	0.230	1.000	0.981	0.000	0.004	0.568	0.543
Contact Map 12 Å	0.335	0.358	0.207	0.251	0.207	0.229	1.000	0.969	0.000	0.001	0.578	0.553
Hierarchical Representation 6Å	0.344	0.348	0.455	0.265	0.231	0.222	0.743	0.950	0.080	0.006	0.588	0.569
Hierarchical Representation 8Å	0.348	0.348	0.384	0.266	0.226	0.222	0.846	0.950	0.073	0.008	0.578	0.556
Hierarchical Representation 10Å	0.340	0.346	0.372	0.262	0.222	0.221	0.833	0.950	0.046	-0.002	0.567	0.551
Hierarchical Representation 12Å	0.332	0.346	0.379	0.262	0.226	0.221	0.804	0.950	0.043	-0.002	0.564	0.542
Other methods
Daberdaku et. al.	0.168	0.151	0.369	0.352	0.095	0.085	0.896	0.846	0.120	0.077	0.720	0.668
SPPIDER											0.726	0.688
NPS-HomPPI											0.646	0.655
PrISE											0.712	0.662

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