Supplemental Material for FoldIndex: Does the Protein Fold?

Individual FoldIndex Scores for the Validation Set Natively Folded and Intrinsically Unfolded Proteins

Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin Rydberg, Orna Man, Jacques S. Beckmann, Israel Silman and Joel L. Sussman

Table 1. FoldIndex Scores for Unfolded Proteins

Protein_ID	Residues	Length	FoldIndex	Log (Disopred)	Pondr VL-XT	GlobProt dy/dx
Unfolded when:			< 0.0	> -2.996	> 0.5	> 0.0
CHTA_VIBCH	25-56	32	-0.218	-2.402	0.718	0.021
IPA3_YEAST	36-68	33	-0.518	-1.646	0.547	-0.020
SYUA_HUMAN	102-138	39	-0.561	-2.490	0.917	0.008
GCN4_YEAST	225-281	57	-0.255	-2.830	0.688	-0.137
KCAB1_RAT	1-62	62	0.048	-2.763	0.373	-0.073
P73124_SYNY3	All	64	-0.051	-3.042	0.515	-0.086
CDNB_HUMAN	22-97	75	-0.263	-3.353	0.447	-0.029
RL11_ECOLI	66-141	76	0.172	-3.880	0.644	-0.074
CGB1_HUMAN	1-78	78	-0.141	-3.016	0.633	-0.039
CHPR_ECOLI	All	82	0.076	-4.082	0.574	-0.069
YEFM_ECOLI	All	83	0.074	-4.083	0.611	-0.091
Cerevisiae_GII	All	84	-0.057	-3.586	0.301	-0.044
BIMC_EMENI	1-89	89	-0.133	-2.211	0.845	-0.045
CEAN_ECOLI	All	90	-0.209	-1.577	0.547	0.129
FOS_HUMAN	216-310	95	0.015	-2.779	0.637	0.011
P53_HUMAN	1-93	103	-0.073	-3.398	0.781	0.029
Q9NR00_HUMAN	All	106	-0.084	-3.273	0.512	-0.103
SECU_YEAST	1-109	109	-0.148	-2.652	0.430	-0.007
PTMA_HUMAN	All	110	-0.779	-3.137	0.864	-0.035
Q83705_9PARA	400-525	126	-0.174	-1.880	0.696	-0.026
H3_ENCAL	All	135	-0.084	-3.367	0.627	-0.108
CALD_CHICK	636-771	136	-0.103	-2.447	0.513	0.006
MAX_HUMAN	All	160	-0.193	-1.967	0.725	-0.058
CAVP_BRALA	All	161	-0.068	-4.096	0.512	-0.065
CDN1A_HUMAN	All	164	-0.038	-2.070	0.555	-0.004
DH1_MAIZE	All	168	-0.142	-3.099	0.717	0.053
MB3_BOVINE	All	169	-0.199	-2.141	0.385	0.023
STN4_HUMAN	All	189	-0.043	-3.426	0.476	-0.111
PRIO_MESAU	29-231	202	-0.125	-3.874	0.558	0.036
SN25_CHICK	All	206	-0.094	-2.697	0.547	-0.077
Q9NK80_DROME	749-956	207	-0.051	-1.779	0.730	-0.030
GIR2_YEAST	All	265	-0.151	-3.968	0.425	-0.099
DAG1_MOUSE	485-750	266	0.059	-4.030	0.332	-0.034
SSO1_YEAST	All	290	0.016	-2.860	0.473	-0.117
CDNC_HUMAN	All	316	0.164	-2.365	0.716	-0.010
MARCKS_HUMAN	All	331	-0.069	-1.681	0.828	-0.018
GCR_HUMAN	1-500	500	0.069	-2.369	0.466	-0.004
NUP2_YEAST	All	720	-0.038	-1.113	0.375	-0.008
TAU_HUMAN	All	757	-0.041	-0.945	0.747	0.029

The second line of the table gives the cutoff criteria between unfolded and folded proteins for each method. The false predictions are colored red, and indeterminant cases are in blue.

Table 2. FoldIndex Scores for Folded Proteins

PDB-ID	Length	FoldIndex	Log (Disopred)	Pondr VL-XT	GlobProt dy/dx
Unfolded when:		< 0.0	> -2.996	> 0.5	> 0.0
1ifj	50	0.354	-4.145	0.297	-0.102
1ifk	51	0.366	-4.085	0.322	-0.111
1kfn	53	-0.078	-2.082	0.559	-0.054
1ifl	53	0.332	-4.265	0.313	-0.109
1enh	54	-0.263	-4.721	0.504	-0.106
1em7	56	-0.060	-4.829	0.270	-0.073
1pga	56	-0.026	-4.618	0.185	-0.061
1mhn	59	0.102	-5.208	0.252	-0.057
1vie	60	0.132	-3.632	0.427	-0.033
1l2p	61	-0.169	-2.800	0.842	-0.162
1igd	61	0.044	-4.939	0.122	-0.061
1i2t	61	0.274	-5.011	0.390	-0.115
2era	62	-0.001	-4.376	0.185	0.014
1r69	63	0.048	-4.305	0.453	-0.073
1coa	64	0.209	-5.572	0.406	-0.106
1ops	64	0.263	-4.441	0.450	-0.057
1ucs	64	0.351	-4.196	0.459	-0.086
3msi	66	0.397	-4.148	0.527	-0.077
1qr9	68	-0.016	-4.052	0.359	-0.090
1df5	68	-0.007	-3.995	0.346	-0.091
3il8	68	0.024	-4.003	0.437	-0.073
1mjc	69	0.140	-4.403	0.213	-0.015
1ail	70	0.089	-3.951	0.364	-0.077
1utg	70	0.128	-4.546	0.363	-0.059
1ubi	76	0.090	-5.177	0.451	-0.058
1vcc	77	0.092	-5.072	0.196	-0.072
1pht	83	-0.092	-4.146	0.369	-0.028
1a32	85	-0.116	-4.324	0.710	-0.112
1cm2	85	0.154	-5.024	0.323	-0.088
1gvp	87	0.161	-4.132	0.284	-0.052
1nfj	87	0.194	-4.947	0.496	-0.109
1fna	91	0.223	-4.275	0.417	-0.025
2ygs	92	0.059	-3.995	0.412	-0.096
1who	94	0.021	-4.803	0.305	-0.053
1lpl	95	0.107	-4.214	0.294	-0.049
1n7e	95	0.242	-4.010	0.351	-0.057
1cdz	96	0.042	-4.817	0.198	-0.074
1jyu	96	0.093	-4.580	0.266	-0.080
1pdr	96	0.183	-4.185	0.459	-0.065
1ris	97	0.058	-4.796	0.467	-0.123
1jwo	97	0.147	-4.837	0.261	-0.069
1bm8	99	0.024	-5.370	0.256	-0.096
1cqy	99	0.044	-4.808	0.283	-0.050
2pcy	99	0.131	-4.369	0.340	-0.017
1sip	99	0.252	-5.106	0.315	-0.047
3phv	99	0.286	-4.917	0.281	-0.063
1tul	102	0.193	-5.484	0.118	-0.093
1p1l	102	0.198	-5.504	0.326	-0.126
1gxq	105	0.067	-5.173	0.470	-0.077
1erv	105	0.154	-5.208	0.198	-0.082
1aaj	105	0.163	-4.310	0.210	-0.073
1auc	105	0.164	-5.240	0.176	-0.084
1ew4	106	-0.074	-5.116	0.193	-0.063
1a1x	106	0.019	-4.222	0.296	-0.092
1bfs	106	0.040	-4.400	0.249	-0.061
1bkr	108	0.095	-4.901	0.164	-0.062
1ar2	109	0.113	-4.839	0.307	-0.034
1pxf	111	0.194	-5.299	0.363	-0.109
1pil	112	0.217	-4.993	0.317	-0.090
1tmy	118	0.258	-5.980	0.287	-0.109
1dhn	121	0.088	-5.534	0.411	-0.089
1qto	122	0.103	-5.271	0.353	-0.049
1whi	122	0.108	-4.821	0.514	-0.079
1byl	122	0.151	-5.337	0.217	-0.075
1pzc	122	0.198	-4.564	0.249	-0.070
1rat	124	0.004	-4.222	0.290	-0.048
1bgf	124	0.135	-4.360	0.282	-0.125
1p6p	125	0.077	-5.094	0.301	-0.068
2acg	125	0.242	-5.242	0.200	-0.066
1acf	125	0.285	-5.172	0.163	-0.058
1k40	126	0.210	-4.374	0.344	-0.117
1jb3	127	0.108	-4.489	0.270	-0.076
2bfh	128	-0.039	-4.207	0.341	-0.058
2chf	128	0.224	-5.679	0.294	-0.097
1uie	129	0.040	-4.517	0.202	-0.029
1uid	129	0.048	-4.608	0.188	-0.033
1msc	129	0.219	-4.364	0.311	-0.071
1loz	130	0.017	-4.579	0.256	-0.062
1a0k	130	0.116	-4.963	0.235	-0.043
1ifb	131	0.063	-4.819	0.256	-0.082
1ab0	131	0.122	-4.991	0.393	-0.072
1lmi	131	0.220	-4.204	0.304	-0.037
1lpj	133	0.037	-4.962	0.256	-0.071
1ahq	133	0.062	-4.570	0.302	-0.080
1kqx	134	0.007	-4.713	0.192	-0.089
1is5	134	0.119	-5.007	0.137	-0.065
1aqt	135	0.144	-4.961	0.493	-0.093
1eqv	136	-0.047	-4.660	0.245	-0.077
1iuk	136	0.159	-5.502	0.421	-0.078
1enk	137	0.096	-4.870	0.304	-0.103
1fso	138	0.116	-4.666	0.296	-0.070
1anu	138	0.261	-4.456	0.141	-0.041
1q2y	140	0.076	-5.792	0.378	-0.090
1h3q	140	0.130	-4.704	0.130	-0.073
1o8w	143	0.107	-4.689	0.231	-0.067
1c3k	143	0.254	-4.882	0.216	-0.031
1qqh	144	-0.029	-5.133	0.111	-0.052
1lpe	144	0.044	-3.520	0.553	-0.144
1j7g	144	0.179	-4.849	0.222	-0.089
1vls	146	0.065	-3.495	0.364	-0.089
1jmw	146	0.070	-3.695	0.358	-0.091
1vsm	146	0.125	-4.963	0.346	-0.078
1aly	146	0.165	-3.878	0.141	-0.064
1ng6	148	0.084	-3.514	0.627	-0.107
1qcq	148	0.131	-4.395	0.241	-0.022
1div	149	0.032	-4.625	0.305	-0.106
2aak	150	0.054	-4.890	0.371	-0.023
1npk	150	0.242	-4.829	0.292	-0.067
1jl1	152	0.009	-4.337	0.440	-0.078
1dvo	152	0.018	-3.919	0.465	-0.109
1byr	152	0.153	-5.364	0.393	-0.075
2i1b	153	0.080	-3.858	0.252	-0.062
2rn2	155	0.033	-4.270	0.391	-0.073
1rbv	155	0.051	-4.465	0.390	-0.074
1jyh	155	0.069	-4.852	0.207	-0.072
2e2c	156	0.042	-4.448	0.252	-0.040
1j85	156	0.116	-5.310	0.350	-0.071
1bd8	156	0.186	-5.833	0.319	-0.074
1kxa	158	0.098	-4.215	0.315	-0.034
1gpr	158	0.161	-4.824	0.402	-0.046
1u9a	160	0.054	-4.695	0.254	-0.039
2itg	160	0.189	-4.640	0.169	-0.084
1c25	161	0.086	-4.136	0.197	-0.070
1ble	161	0.227	-4.972	0.352	-0.103
2abl	163	0.064	-3.920	0.258	-0.034
2ucz	164	0.118	-4.872	0.337	-0.029
1g5z	164	0.131	-4.237	0.245	-0.105
2cpl	164	0.133	-4.890	0.198	-0.026
1c3g	170	-0.068	-4.194	0.403	-0.016
1oxj	170	0.185	-3.975	0.359	-0.100
1dyw	172	0.118	-4.955	0.186	-0.014
261l	173	0.058	-4.452	0.292	-0.087
1qoi	173	0.194	-4.884	0.196	-0.027
1gcs	174	-0.009	-5.136	0.152	-0.044
1igp	175	0.093	-5.580	0.305	-0.063
1mjz	175	0.108	-5.520	0.282	-0.065
1bef	177	0.101	-4.487	0.358	-0.027
1a58	177	0.170	-4.712	0.158	-0.035
1ilw	179	0.108	-5.560	0.312	-0.072
1zon	181	0.156	-4.289	0.161	-0.097
1dov	181	0.164	-4.469	0.343	-0.114
1ep0	183	0.001	-5.655	0.286	-0.068
1c5h	185	0.033	-4.815	0.131	0.005
1eh1	185	0.060	-4.358	0.512	-0.107
1is1	185	0.093	-4.405	0.644	-0.103
1ad6	185	0.198	-4.251	0.259	-0.105
1n81	186	0.041	-4.686	0.327	-0.113
1eq6	189	0.078	-4.284	0.356	-0.100
1xnd	190	0.076	-4.712	0.143	0.002
1na5	195	0.105	-4.215	0.259	-0.079
1pbv	195	0.106	-4.609	0.363	-0.076