Frequency of each amino acid in the metal ion–binding sites.

<p>Frequencies of each amino acid in a given type of metal ion–binding site (black) and in the corresponding protein (grey). <b>A</b>, Ca²⁺. <b>B</b>, Cu²⁺. <b>C</b>, Fe³⁺. <b>D</b>, Mg²⁺. <b>E</b>, Mn²⁺. <b>F</b>, Zn²⁺. For this study, 1,109 metal ion–binding polypeptides were used and the metal ion–binding sites were defined as residues partially within 3.5 Å of the metal ion.</p

Frequency of atom types in the metal ion–binding sites.

<p>Frequency of each type of atom in the backbone (black) and in the side chain (grey). <b>A</b>, Ca²⁺. <b>B</b>, Cu²⁺. <b>C</b>, Fe³⁺. <b>D</b>, Mg²⁺. <b>E</b>, Mn²⁺. <b>F</b>, Zn²⁺.</p

Identification of Ca²⁺–binding sites.

<p><b>A</b>. human cytosolic phospholipase A2 (PDB ID∶1RLW) as the query protein. <b>B</b>. Template constructed from chain A of synaptotagmin I C2B-domain (PDB ID∶1K5W).</p

Comparison of the results for the fragment transformation and the artificial neural network methods.

<p>Comparison of the results for the fragment transformation and the artificial neural network methods.</p

The fragment transformation method.

<p><i>σ_i</i> and <i>σ_k</i> are two arbitrary triplet units in the query protein <i>S</i>, and <i>τ_j</i> and <i>τ_l</i> are two arbitrary triplet units in the template <i>T</i>. In the illustration, the triplet <i>σ_i</i> is transformed onto <i>τ_j</i> via application of the transformation matrix <i>M_i,j</i>.</p

Identification of Mg²⁺–binding sites.

<p><b>A</b>. Chain A of human mitochondrial deoxyribonucleotidase (PDB ID∶1MH9) as the query protein. <b>B</b>. Template constructed from chain B of transglutaminase 3 (PDB ID∶1NUG).</p

Schematic of the metal ion–binding prediction method.

<p>Schematic of the metal ion–binding prediction method.</p

Receiver operating characteristic curves generated from the metal ion–binding site prediction.

<p>The performance of the method was assessed by measuring the areas under the receiver operating characteristic curves. The <i>x</i> axis reports the false positive rate (FPR), and the <i>y </i>axis reports the true positive rate (TPR).</p

Metal ion–binding residues.

<p>All residues at least partially within 3.5 Å of a metal ion are defined as metal ion–binding residues.</p

The types and number of metal ion–binding polypeptides and metal ion–binding residue template.

<p>The types and number of metal ion–binding polypeptides and metal ion–binding residue template.</p