Comparison of two FAD binding sites including side chain information.

<p>The same binding pockets depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011988#pone-0011988-g003" target="_blank">Figure 3</a> were compared using a description that includes side-chain information. The residues comprising the β-sheets were not used in the comparison. See text for details.</p

Alternative residue representations.

<p>Three alternative ways to represent histidine, along with the corresponding syntax used by superpose3D. The atoms are named according to the PDB standard. The “avg(ND1,ND2):bar” statement (middle) defines a pseudoatom named “bar” whose coordinates correspond to the geometric centroid of the ND1 and NE2 atoms. The “\N;\O” statement (right) specifies that all the atoms that contain an “N” or “O” in their names should be included in the representation.</p

Superimposed ligands and matching pseudoatoms.

<p>The ligands of serine racemase from <i>Schizosaccharomyces pombe</i> (2zpu) and Argininosuccinate synthetase from <i>Thermus thermophilus</i> (1kor) superimposed according to the binding site similarity identified by superpose3D. This residue description uses pseudoatoms representing specific side-chain groups. The matching pseudoatoms are shown as spheres. 2zpu is shown with darker colors.</p

Two enzymes with similar substrate binding sites.

<p>The figure depicts the active sites of the teichoic acid phosphorylcholine esterase Pce from <i>Streptococcus pneumoniae</i> (2bib, left) and a methionine aminopeptidase from <i>Escherichia coli</i> (2gg8, right). These unrelated enzymes use similar mechanisms and have analogous binding modes for the substrate (left) and an inhibitor (right).</p

Comparison of two metal coordination sites.

<p>The proeins involved are Lysyl oxidase from <i>Pichia pastoris</i> (1w7c, left) and rabbit glycogenin-1 (1ll2, right).</p

Comparison of two anion binding loops.

<p>The loop on the left binds phosphate while the right one binds the O2 and O3′ of the riboflavine moiety of FAD. Left: dethiobiotin synthetase from <i>Escherichia coli</i> (1dak); right: D-amino acid oxidase from the yeast <i>Rhodotorula gracilis</i> (1c0i). In this figure and in the following ones protein residues are represented as sticks and ligands as ball and sticks. Moreover ligand names are written in bold.</p

Comparison of two FAD binding sites.

<p>The two binding pockets belong to proteins of different Rossmann-like folds. Left: human monoamine oxidase B (2v61); right: Electron transfer flavoprotein from <i>Methylophilus methylotrophus</i> (3clt). The central β-sheets that characterize these structures are shown in the picture but only the binding site residues were used in the comparison.</p

Etude numérique de la statistique des champs locaux : tailles de VER

International audienc

Output page of a FunClust search in four non-homologous serine protease protein chains (1a0jA, 1sca, 1tyfA and 1e5tA)

The three different clusters identified are shown in tabular form. For each cluster the associated score is reported. The right section of each table reports, in each row, the residues belonging to the different structures, with structurally aligned residues written in the same column. The left section shows the r.m.s.d. value for each match identified between the structures corresponding to the row and column of the table (recall that two structures belonging to the cluster do not necessarily match to each other). In the example shown, the first of the three clusters is composed of the four catalytic triads which are therefore correctly identified. The second cluster identifies three non-catalytic residues in structure 1e5t, while the third one (with the lowest score) involves only three of the four structures. A user activated popup window shows a graphical view (created using the Jmol applet) of the first cluster. The four different structures have been superposed on the residues belonging to the structural motif. Each structure has a different colour, and only the residues involved in the cluster are shown. Commands to trigger the display of the whole structure and of the labels for each protein in the cluster are located in the right portion of the window.<p><b>Copyright information:</b></p><p>Taken from "FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures"</p><p>http://www.biomedcentral.com/1471-2105/9/S2/S2</p><p>BMC Bioinformatics 2008;9(Suppl 2):S2-S2.</p><p>Published online 26 Mar 2008</p><p>PMCID:PMC2323665.</p><p></p

F-score of the method at different R.M.S.D. thresholds.

<p>Average F-scores of the method (considering all the nucleotide types) for each nucleotide module and for each R.M.S.D. threshold used during the structural comparison step.</p