Table 1.

Correlation of B-factors and predictions by simple models for a set of 30 proteins

PDB ID	No. of residues	CorrGNM	CorrEPIRM	CorrANM
1e44	180	0.587	0.586	0.410
1eai	602	0.650	0.656	0.647
1ega	585	0.562	0.563	0.503
1ep9	320	0.671	0.669	0.668
1gk1	1350	0.631	0.655	0.309
1gpw	1359	0.471	0.468	0.279
1hi9	1370	0.453	0.456	0.319
1i1r	468	0.464	0.507	0.302
1i8t	734	0.777	0.774	0.752
1job	162	0.745	0.738	0.686
1kiy	708	0.640	0.630	0.620
1kkh	317	0.401	0.397	0.059
1l5j	1724	0.583	0.575	0.546
1lbq	710	0.713	0.704	0.690
1lq8	1431	0.632	0.627	0.597
1n26	299	0.530	0.516	0.504
1nbw	1436	0.563	0.557	0.485
1nd6	1369	0.732	0.724	0.683
1o9h	249	0.459	0.473	0.233
1oe0	792	0.694	0.693	0.651
1oia	176	0.695	0.694	0.421
1okr	242	0.507	0.518	0.331
1ot5	956	0.677	0.675	0.653
1q19	2000	0.578	0.568	0.574
1qgo	257	0.527	0.512	0.489
1ql6	281	0.642	0.634	0.594
1qpo	1704	0.627	0.620	0.60
1spp	221	0.581	0.585	0.567
2gsa	854	0.319	0.318	0.308
2tdx	139	0.613	0.605	0.521
Mean		0.591 ± 0.020	0.590 ± 0.019	0.500 ± 0.031

The 30 nonhomologous proteins are a subset of a previously reported representative set (36). They share no sequence identity (<30%) or structural homology (C_α RMSD >10 Å). The proteins are resolved by x-ray crystallography with a resolution of ≤2.4 Å and an R-factor of ≤0.3, containing no membrane or small (N < 40) proteins. The mean ± standard errors values are listed in the bottom row of the table. Here, a uniform 15-Å cutoff is chosen for the three models to ensure equal sparsity in Hessians. The means drop slightly to 0.57 for both GNM and EPIRM if a cutoff of 7.5 Å is used. Corr, correlation between predictions of physical models and the experimental observables; PDB, Protein Data Bank.