Table 3 

Discriminatory power of structure and sequence derived quantities 

Numerical index 
Thermophile (127 pairs) 
Hyperthermophile (122 pairs) 


Contact Network Derived Quantities 

coordination number (no cutoff) 
0.559 
0.689 
clustering coefficient (no cutoff) 
0.551 
0.672 
characteristic path (no cutoff) 
0.520 
0.631 
Combined Sequence and Structure Including Threading Potentials 

total count 400 overrep quads/residue 
0.850 
0.943 
4body potential/residue (20Å cutoff) 
0.858 
0.844 
4body potential/residue (no cutoff) 
0.843 
0.852 
4body potential/res (hyper only, no cutoff) 
 
0.820 
4body potential/res (meso only, no cutoff) 
0.732 
0.803 
4body potential/res (thermo only,no cutoff) 
0.866 
 
ProsaII combined score 
0.554 
0.693 
Delaunay Simplex Geometry 

median circumsphere radius(no cutoff) 
0.701 
0.639 
mean tetrahedrality (no cutoff) 
0.598 
0.574 
number simplices/residue (10Å cutoff) 
0.528 
0.557 
number simplices/residue (no cutoff) 
0.567 
0.697 
Volume/Surface Area/Compactness 

Naccess solvent accessible area 
0.567 
0.598 
Delaunay surface area (no cutoff) 
0.606 
0.669 
van der Waals area 
0.559 
0.549 
Delaunay volume (no cutoff) 
0.598 
0.701 
Van der Waals volume 
0.528 
0.598 
Delaunay area/volume (10Å cutoff) 
0.583 
0.549 
Delaunay area/volume (no cutoff) 
0.669 
0.803 
van der Waals area/volume 
0.512 
0.557 
packing density 
0.543 
0.549 
van der Waals volume/Delaunay volume 
0.685 
0.779 
Rigidity 

mean Bfactor 
0.661 
0.533 
Secondary Structure 

secondary structure content (H+E 3 state DSSP) 
0.614 
0.689 
Sequence Length 

number of residues 
0.528 
0.672 
Sequence Composition 

total KyteDoolittle hydrophobicity 
0.575 
0.549 
sd KyteDoolittle hydrophobicity 
0.677 
0.836 
CvP bias 
0.803 
0.918 
(E+K)/(Q+H) 
0.591 
0.861 
IVYWREL 
0.827 
0.926 


A table showing the discriminatory power of sequence and structure based indicesthe fraction of thermophile/mesophile pairs for which the quantity was systematically higher or lower by any amount. The contact network quantities are described in the introduction. The four body threading contact potentials are described in [1]. The cutoff indicates that simplices with at least one edge longer than the cutoff were omitted when frequencies are tallied during the calculation of the potential. "Hyper only" indicates that the potential was trained only on chains from hyperthermophilic organisms. The Delaunay simplex geometry indices are discussed in the introduction. The volume and surface area criteria are fairly selfexplanatory except, perhaps, for packing density that is defined here as the ratio of the van der Waals volume of the protein divided by the all atom Voronoi volume. The sequence composition based indices CvP, (E+K)/(Q+H), and IVYWREL are described in the introduction. 

Taylor and Vaisman BMC Structural Biology 2010 10(Suppl 1):S5 doi:10.1186/1472680710S1S5 