Reglas generales para el empleo de los signos de puntuación

Mención de responsabilidad tomada de la cubiert

Examples of typical coordination bonds between metal ions and Cys and His residues.

<p>Coordination bonds are represented by solid lines; the dashed lines show the distance between atoms of different residues. Panel A shows the coordination bond between zinc ion and four Cys residues where sulfur atom is shown in gray, carbon atom in white, and zinc ion in black. The sulfur atoms of four Cys residues form an approximate regular tetrahedron and the zinc ion is located in its center. Panel B shows the coordination bond between zinc ion and three His residues. The nitrogen atoms are shown in gray, other atoms of the His side chain are in white, and zinc ion is colored black. The three nitrogen atoms form an approximate equilateral triangle with the length of the sides that varies between 3.14 Å and 3.31 Å. The zinc ion is not located on the triangle plane.</p

The residue groups that are coordinated by at least 10 metal ions and consist of 2 residues.

<p>The residue groups that are coordinated by at least 10 metal ions and consist of 2 residues.</p

Percentage of occurrence of amino acids in the protein-organic compound binding pockets (gray bar) and in protein-protein interaction interfaces (black bar).

<p>Percentage of occurrence of amino acids in the protein-organic compound binding pockets (gray bar) and in protein-protein interaction interfaces (black bar).</p

A summary of interaction patterns concerning covalent bonds formed between a protein and an organic compound.

1<p>The patterns are shown in X^R – Y^L format where X denotes an atom type of residue R in the protein and Y denotes an atom type of the ligand L.</p

An overview of the protein pocket-ligand interactions.

<p>The top layer divides protein-ligand complexes into 5 major groups based on the type of the ligand. The second layer shows the major forces that are involved in formation of protein-ligand complexes for each type of the ligand. The bottom layer summarizes significant (frequently occurring) patterns for each force/bond type and each type of the ligand. The patterns are shown in X^R…Y^L or X^R – Y^L format where X denotes an atom type of residue R in the protein, Y denotes an atom type of the ligand L, strong interactions (covalent and coordination bonds) are depicted by “–”, and weak interactions (hydrogen bond) are represented by “…”.</p

A summary of the coordination bonds between metal ions and a given number of residues in a protein pocket that contribute at least one atom to form the bond.

<p>A summary of the coordination bonds between metal ions and a given number of residues in a protein pocket that contribute at least one atom to form the bond.</p

A summary of hydrogen bonds formed between specific amino acids and organic compounds.

1<p>the hydropathy index values from reference 26; the larger (smaller) the index values is, the more hydrophobic (hydrophilic) the amino acid.</p>2<p>the percentages of hydrogen bonds between specific amino acids and DNA molecules were taken from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004473#pone-0004473-t002" target="_blank">Table 2</a> of reference 5.</p

The residue groups that are coordinated by at least 10 metal ions and consist of 3 residues.

<p>The residue groups that are coordinated by at least 10 metal ions and consist of 3 residues.</p

Performance of blind binding site predictors including the pattern-based method, Ligsite^CSC, and a random baseline predictor.

<p>The <i>y</i> axis shows success rate, i.e., fraction of proteins with minimum distance between the top five predicted binding sites and any atom of a ligand in the native complex that is smaller or equal to the distance displayed on the <i>x</i> axis. The five plots concern the scanning method based solely on the hydrogen bond pattern (named “Scanning (hydrogen)”), the scanning method based on the four patterns concerning both hydrogen and covalent bonds (named “Scanning (hydrogen&covalent)”), the result of Ligsite^CSC, the result of baseline method that randomly picks 5 solvent grid points that are within 5Å from the protein surface (named “Random baseline”), and the results that merge the top two predictions of Ligsite^CSC and the top three predictions of the scanning method that uses the four patterns (named “Scanning/Ligsite-csc hybrid”).</p