Table V.

Correlation coefficients for B-factor prediction obtained by optimal FRI (opFRI), parameter free FRI (pfFRI), and Gaussian normal mode (GNM) for a set of 365 proteins. GNM scores reported here are the result of our tests with a processed set of PDB files as described in Sec. III C.

PDB ID	N	opFRI	pfFRI	GNM	PDB ID	N	opFRI	pfFRI	GNM
1ABA	87	0.727	0.698	0.613	1PEF	18	0.888	0.826	0.808
1AGN	1492	0.331	0.051	0.170	1PEN	16	0.516	0.465	0.270
1AHO	64	0.698	0.625	0.562	1PMY	123	0.671	0.654	0.685
1AIE	31	0.588	0.416	0.155	1PZ4	114	0.828	0.781	0.843
1AKG	16	0.373	0.350	0.185	1Q9B	43	0.746	0.726	0.656
1ATG	231	0.613	0.578	0.497	1QAU	112	0.678	0.672	0.620
1BGF	124	0.603	0.539	0.543	1QKI	3912	0.809	0.751	0.645
1BX7	51	0.726	0.623	0.706	1QTO	122	0.543	0.520	0.334
1BYI	224	0.543	0.491	0.552	1R29	122	0.650	0.631	0.556
1CCR	111	0.580	0.512	0.351	1R7J	90	0.789	0.621	0.368
1CYO	88	0.751	0.702	0.741	1RJU	36	0.517	0.447	0.431
1DF4	57	0.912	0.889	0.832	1RRO	112	0.435	0.372	0.529
1E5K	188	0.746	0.732	0.859	1SAU	114	0.742	0.671	0.596
1ES5	260	0.653	0.638	0.677	1TGR	104	0.720	0.711	0.714
1ETL	12	0.710	0.609	0.628	1TZV	141	0.837	0.820	0.841
1ETM	12	0.544	0.393	0.432	1U06	55	0.474	0.429	0.434
1ETN	12	0.089	0.023	−0.274	1U7I	267	0.778	0.762	0.691
1EW4	106	0.650	0.644	0.547	1U9C	221	0.600	0.577	0.522
1F8R	1932	0.878	0.859	0.738	1UHA	83	0.726	0.665	0.638
1FF4	65	0.718	0.613	0.674	1UKU	102	0.665	0.661	0.742
1FK5	93	0.590	0.568	0.485	1ULR	87	0.639	0.594	0.495
1GCO	1044	0.766	0.693	0.646	1UOY	64	0.713	0.653	0.671
1GK7	39	0.845	0.773	0.821	1USE	40	0.438	0.146	-0.142
1GVD	52	0.781	0.732	0.591	1USM	77	0.832	0.809	0.798
1GXU	88	0.748	0.634	0.421	1UTG	70	0.691	0.610	0.538
1H6V	2927	0.488	0.429	0.306	1V05	96	0.629	0.599	0.632
1HJE	13	0.811	0.686	0.616	1V70	105	0.622	0.492	0.162
1I71	83	0.549	0.516	0.549	1VRZ	21	0.792	0.695	0.677
1IDP	441	0.735	0.715	0.690	1W2L	97	0.691	0.564	0.397
1IFR	113	0.697	0.689	0.637	1WBE	204	0.591	0.577	0.549
1K8U	89	0.553	0.531	0.378	1WHI	122	0.601	0.539	0.270
1KMM	1499	0.749	0.744	0.558	1WLY	322	0.695	0.679	0.666
1KNG	144	0.547	0.536	0.512	1WPA	107	0.634	0.577	0.417
1KR4	110	0.635	0.612	0.466	1X3O	80	0.600	0.559	0.654
1KYC	15	0.796	0.763	0.754	1XY1	18	0.832	0.645	0.447
1LR7	73	0.679	0.657	0.620	1XY2	8	0.619	0.570	0.562
1MF7	194	0.687	0.681	0.700	1Y6X	87	0.596	0.524	0.366
1N7E	95	0.651	0.609	0.497	1YJO	6	0.375	0.333	0.434
1NKD	59	0.750	0.703	0.631	1YZM	46	0.842	0.834	0.901
1NKO	122	0.619	0.535	0.368	1Z21	96	0.662	0.638	0.433
1NLS	238	0.669	0.530	0.523	1ZCE	146	0.808	0.757	0.770
1NNX	93	0.795	0.789	0.631	1ZVA	75	0.756	0.579	0.690
1NOA	113	0.622	0.604	0.615	2A50	457	0.564	0.524	0.281
1NOT	13	0.746	0.622	0.523	2AGK	233	0.705	0.694	0.512
1O06	20	0.910	0.874	0.844	2AH1	939	0.684	0.593	0.521
1O08	221	0.562	0.333	0.309	2B0A	186	0.639	0.603	0.467
1OB4	16	0.776	0.763	0.750	2BCM	413	0.555	0.551	0.477
1OB7	16	0.737	0.545	0.652	2BF9	36	0.606	0.554	0.680
1OPD	85	0.555	0.409	0.398	2BRF	100	0.795	0.764	0.710
1P9I	29	0.754	0.742	0.625	2C71	205	0.658	0.649	0.560
2CE0	99	0.706	0.598	0.529	2OLX	4	0.917	0.888	0.885
2CG7	90	0.551	0.539	0.379	2PKT	93	0.162	0.003	−0.193
2COV	534	0.846	0.823	0.812	2PLT	99	0.508	0.484	0.509
2CWS	227	0.647	0.640	0.696	2PMR	76	0.693	0.682	0.619
2D5W	1214	0.689	0.682	0.681	2POF	440	0.682	0.651	0.589
2DKO	253	0.816	0.812	0.690	2PPN	107	0.677	0.638	0.668
2DPL	565	0.596	0.538	0.658	2PSF	608	0.526	0.500	0.565
2DSX	52	0.337	0.333	0.127	2PTH	193	0.822	0.784	0.767
2E10	439	0.798	0.796	0.692	2Q4N	153	0.711	0.667	0.740
2E3H	81	0.692	0.682	0.605	2Q52	412	0.756	0.748	0.621
2EAQ	89	0.753	0.690	0.695	2QJL	99	0.594	0.584	0.594
2EHP	248	0.804	0.804	0.773	2R16	176	0.582	0.495	0.618
2EHS	75	0.720	0.713	0.747	2R6Q	138	0.603	0.540	0.529
2ERW	53	0.461	0.253	0.199	2RB8	93	0.727	0.614	0.517
2ETX	389	0.580	0.556	0.632	2RE2	238	0.652	0.613	0.673
2FB6	116	0.791	0.786	0.740	2RFR	154	0.693	0.671	0.753
2FG1	157	0.620	0.617	0.584	2V9V	135	0.555	0.548	0.528
2FN9	560	0.607	0.595	0.611	2VE8	515	0.744	0.643	0.616
2FQ3	85	0.719	0.692	0.348	2VH7	94	0.775	0.726	0.596
2G69	99	0.622	0.590	0.436	2VIM	104	0.413	0.393	0.212
2G7O	68	0.785	0.784	0.660	2VPA	204	0.763	0.755	0.576
2G7S	190	0.670	0.644	0.649	2VQ4	106	0.680	0.679	0.555
2GKG	122	0.688	0.646	0.711	2VY8	149	0.770	0.724	0.533
2GOM	121	0.586	0.584	0.491	2VYO	210	0.675	0.648	0.729
2GXG	140	0.847	0.780	0.520	2W1V	548	0.680	0.680	0.571
2GZQ	191	0.505	0.382	0.369	2W2A	350	0.706	0.638	0.589
2HQK	213	0.824	0.809	0.365	2W6A	117	0.823	0.748	0.647
2HYK	238	0.585	0.575	0.510	2WJ5	96	0.484	0.440	0.357
2I24	113	0.593	0.498	0.494	2WUJ	100	0.739	0.598	0.598
2I49	398	0.714	0.683	0.601	2WW7	150	0.499	0.471	0.356
2IBL	108	0.629	0.625	0.352	2WWE	111	0.692	0.582	0.628
2IGD	61	0.585	0.481	0.386	2X1Q	240	0.534	0.478	0.443
2IMF	203	0.652	0.625	0.514	2X25	168	0.632	0.598	0.403
2IP6	87	0.654	0.578	0.572	2X3M	166	0.744	0.717	0.655
2IVY	88	0.544	0.483	0.271	2X5Y	171	0.718	0.705	0.694
2J32	244	0.863	0.848	0.855	2X9Z	262	0.583	0.578	0.574
2J9W	200	0.716	0.705	0.662	2XHF	310	0.606	0.591	0.569
2JKU	35	0.805	0.695	0.656	2Y0T	101	0.778	0.774	0.798
2JLI	100	0.779	0.613	0.622	2Y72	170	0.780	0.754	0.766
2JLJ	115	0.741	0.720	0.527	2Y7L	319	0.928	0.797	0.747
2MCM	113	0.789	0.713	0.639	2Y9F	149	0.771	0.762	0.664
2NLS	36	0.605	0.559	0.530	2YLB	400	0.807	0.807	0.675
2NR7	194	0.803	0.785	0.727	2YNY	315	0.813	0.804	0.706
2NUH	104	0.835	0.691	0.771	2ZCM	357	0.458	0.422	0.420
2O6X	306	0.814	0.799	0.651	2ZU1	360	0.689	0.672	0.653
2OA2	132	0.571	0.456	0.458	3A0M	148	0.807	0.712	0.392
2OCT	192	0.567	0.550	0.540	3A7L	128	0.713	0.663	0.756
2OHW	256	0.614	0.539	0.475	3AMC	614	0.675	0.669	0.581
2OKT	342	0.433	0.411	0.336	3AUB	116	0.614	0.608	0.637
2OL9	6	0.909	0.904	0.689	3B5O	230	0.644	0.629	0.601
3BA1	312	0.661	0.624	0.621	3MD4	12	0.860	0.781	0.914
3BED	261	0.845	0.820	0.684	3MD5	12	0.649	0.413	-0.218
3BQX	139	0.634	0.481	0.297	3MEA	166	0.669	0.669	0.600
3BZQ	99	0.532	0.516	0.466	3MGN	348	0.205	0.119	0.193
3BZZ	100	0.485	0.450	0.600	3MRE	383	0.661	0.641	0.567
3DRF	547	0.559	0.549	0.488	3N11	325	0.614	0.583	0.517
3DWV	325	0.707	0.661	0.547	3NE0	208	0.706	0.645	0.659
3E5T	228	0.502	0.489	0.296	3NGG	94	0.696	0.689	0.719
3E7R	40	0.706	0.687	0.642	3NPV	495	0.702	0.653	0.677
3EUR	140	0.431	0.427	0.577	3NVG	6	0.721	0.617	0.597
3F2Z	149	0.824	0.792	0.740	3NZL	73	0.627	0.583	0.506
3F7E	254	0.812	0.803	0.811	3O0P	194	0.727	0.706	0.734
3FCN	158	0.640	0.606	0.632	3O5P	128	0.734	0.698	0.630
3FE7	91	0.583	0.533	0.276	3OBQ	150	0.649	0.645	0.655
3FKE	250	0.525	0.476	0.435	3OQY	234	0.698	0.686	0.637
3FMY	66	0.701	0.655	0.556	3P6J	125	0.774	0.767	0.810
3FOD	48	0.532	0.440	-0.126	3PD7	188	0.770	0.723	0.589
3FSO	221	0.831	0.817	0.793	3PES	165	0.697	0.642	0.683
3FTD	240	0.722	0.713	0.634	3PID	387	0.537	0.531	0.642
3FVA	6	0.835	0.825	0.789	3PIW	154	0.758	0.744	0.717
3G1S	418	0.771	0.700	0.630	3PKV	221	0.625	0.597	0.568
3GBW	161	0.820	0.747	0.510	3PSM	94	0.876	0.790	0.745
3GHJ	116	0.732	0.511	0.196	3PTL	289	0.543	0.541	0.468
3HFO	197	0.691	0.670	0.518	3PVE	347	0.718	0.667	0.568
3HHP	1234	0.720	0.716	0.683	3PZ9	357	0.709	0.709	0.678
3HNY	156	0.793	0.723	0.758	3PZZ	12	0.945	0.922	0.950
3HP4	183	0.534	0.500	0.573	3Q2X	6	0.922	0.904	0.866
3HWU	144	0.754	0.748	0.841	3Q6L	131	0.622	0.577	0.605
3HYD	7	0.966	0.950	0.867	3QDS	284	0.780	0.745	0.568
3HZ8	192	0.617	0.502	0.475	3QPA	197	0.587	0.442	0.503
3I2V	124	0.486	0.441	0.301	3R6D	221	0.688	0.669	0.495
3I2Z	138	0.613	0.599	0.317	3R87	132	0.452	0.419	0.286
3I4O	135	0.735	0.714	0.738	3RQ9	162	0.510	0.403	0.242
3I7M	134	0.667	0.635	0.695	3RY0	128	0.616	0.606	0.470
3IHS	169	0.586	0.565	0.409	3RZY	139	0.800	0.784	0.849
3IVV	149	0.817	0.797	0.693	3S0A	119	0.562	0.524	0.526
3K6Y	227	0.586	0.535	0.301	3SD2	86	0.523	0.421	0.237
3KBE	140	0.705	0.704	0.611	3SEB	238	0.801	0.712	0.826
3KGK	190	0.784	0.775	0.680	3SED	124	0.709	0.658	0.712
3KZD	85	0.647	0.611	0.475	3SO6	150	0.675	0.666	0.630
3L41	220	0.718	0.716	0.669	3SR3	637	0.619	0.611	0.624
3LAA	169	0.827	0.647	0.659	3SUK	248	0.644	0.633	0.567
3LAX	106	0.734	0.730	0.584	3SZH	697	0.817	0.815	0.697
3LG3	833	0.658	0.614	0.589	3T0H	208	0.808	0.775	0.694
3LJI	272	0.612	0.608	0.551	3T3K	122	0.796	0.748	0.735
3M3P	249	0.584	0.554	0.338	3T47	141	0.592	0.527	0.447
3M8J	178	0.730	0.728	0.628	3TDN	357	0.458	0.419	0.240
3M9J	210	0.639	0.574	0.296	3TOW	152	0.578	0.556	0.571
3M9Q	176	0.591	0.510	0.471	3TUA	210	0.665	0.658	0.588
3MAB	173	0.664	0.591	0.451	3TYS	75	0.853	0.800	0.791
3U6G	248	0.635	0.632	0.526	4DT4	160	0.776	0.738	0.716
3U97	77	0.753	0.736	0.712	4EK3	287	0.680	0.680	0.674
3UCI	72	0.589	0.526	0.495	4ERY	318	0.740	0.701	0.688
3UR8	637	0.666	0.652	0.597	4ES1	95	0.648	0.625	0.551
3US6	148	0.698	0.586	0.553	4EUG	225	0.570	0.529	0.405
3V1A	48	0.531	0.487	0.583	4F01	448	0.633	0.372	0.688
3V75	285	0.604	0.596	0.491	4F3J	143	0.617	0.598	0.551
3VN0	193	0.840	0.837	0.812	4FR9	141	0.671	0.655	0.501
3VOR	182	0.602	0.557	0.484	4G14	15	0.467	0.323	0.356
3VUB	101	0.625	0.610	0.607	4G2E	151	0.760	0.755	0.758
3VVV	108	0.833	0.741	0.753	4G5X	550	0.786	0.754	0.743
3VZ9	163	0.785	0.749	0.695	4G6C	658	0.591	0.590	0.528
3W4Q	773	0.737	0.725	0.649	4G7X	194	0.688	0.587	0.624
3ZBD	213	0.651	0.516	0.632	4GA2	144	0.528	0.485	0.406
3ZIT	152	0.430	0.404	0.392	4GMQ	92	0.678	0.628	0.550
3ZRX	221	0.590	0.562	0.391	4GS3	90	0.544	0.522	0.547
3ZSL	138	0.691	0.687	0.526	4H4J	236	0.810	0.806	0.689
3ZZP	74	0.524	0.460	0.448	4H89	168	0.682	0.588	0.596
3ZZY	226	0.746	0.709	0.728	4HDE	168	0.745	0.728	0.615
4A02	166	0.618	0.516	0.303	4HJP	281	0.703	0.649	0.510
4ACJ	167	0.748	0.746	0.759	4HWM	117	0.638	0.622	0.499
4AE7	186	0.724	0.717	0.717	4IL7	85	0.446	0.404	0.316
4AM1	345	0.674	0.619	0.460	4J11	357	0.620	0.562	0.401
4ANN	176	0.551	0.536	0.470	4J5O	220	0.793	0.757	0.777
4AVR	188	0.680	0.605	0.650	4J5Q	146	0.742	0.742	0.689
4AXY	54	0.700	0.623	0.720	4J78	305	0.658	0.648	0.608
4B6G	558	0.765	0.756	0.669	4JG2	185	0.746	0.736	0.543
4B9G	292	0.844	0.816	0.763	4JVU	207	0.723	0.697	0.553
4DD5	387	0.615	0.596	0.351	4JYP	534	0.688	0.682	0.538
4DKN	423	0.781	0.761	0.539	4KEF	133	0.580	0.530	0.324
4DND	95	0.763	0.750	0.582	5CYT	103	0.441	0.421	0.331
4DPZ	109	0.730	0.726	0.651	6RXN	45	0.614	0.574	0.594
4DQ7	328	0.690	0.683	0.376