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 over-rep quads/residue

0.850

0.943

4-body potential/residue (20Å cutoff)

0.858

0.844

4-body potential/residue (no cutoff)

0.843

0.852

4-body potential/res (hyper only, no cutoff)

-----

0.820

4-body potential/res (meso only, no cutoff)

0.732

0.803

4-body 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 B-factor

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 Kyte-Doolittle hydrophobicity

0.575

0.549

sd Kyte-Doolittle 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 indices-the 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 self-explanatory 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:10.1186/1472-6807-10-S1-S5

Open Data