Distribution of the sensitivity for correctly predicted ligand binding sites ranked as first (blue bar) and in the top three (red bar), respectively, for all protein complexes in the benchmark

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-10

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-1

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-5

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>owest). The structures shown in the left and the right columns are holo and apo proteins, respectively. The known ligand binding site is located in the white circle. The RMSD between the holo and apo protein across the whole structure is shown above the arrow. (A) Immunoglobulin 48g7 germline fab (PDB id: 1AJ7 and 2RCS); (B) Adenylate kinase (PDB id: 1AKE and 4AKE); (C) HIV-1 reverse transcriptase (PDB id: 1VRT and 1RTJ); (D) Maltodextrin binding protein (PDB id: 1ANF and 1OMP)

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-9

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>ison, the prediction from the geometric potential is marked as a solid blue circle. (B) The predicted two largest binding sites from CASTp [29] with Conly representation and probe radius 2.8 Å. The two largest pockets with similar volume and surface area are shown in the figure. The pockets colored green and red represent a known ligand binding site and a helical interface, respectively

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-8

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>above 80%, as shown by the red circle

Distribution of the standard deviations of geometric potential and relative solvent accessible surface area in the binding sites, scaled between 0

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>0 and 100.0

See Methods and Figure 3 for the definition of the specificity and the sensitivity

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-0

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>the algorithm. (1) Step 1: the protein structure is represented as Cá atoms. (2) Step 2: Cá atoms are Delaunay tessellated. The convex hull is determined at the same time. (3) Step 3: the environmental boundary (red solid lines) is determined from the Delaunay tessellation by peeling off the tetrahedra (triangles labeled as a, b, and c) with edge lengths larger than 30.0 Å (black dashed lines) starting from the convex hull. (4) Step 4: the protein boundary (blue and purple solid lines). The purple lines are overlapped with the environmental boundary and determined from the Delaunay tessellation by removing tetrahedra with circumscribed sphere radius larger than 7.5 Å. (5) Step 5–7: shape descriptors such as residue surface direction and geometric potential for each Cá atom position are computed and ligand binding sites and virtual atoms (open circle) are predicted

Views of Structural Representatives from Six Families in the Kinase-Like Superfamily Other Than the TPKs

<p>Structures are shown in an open-face view, and using the same conventions as used for PKA in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>. ATP and metal ions are shown in mirror image where available in the structure. Similar to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>, secondary structural elements are colored according to their conservation status in the overall superfamily as follows: yellow, elements are part of the “universal core” seen in all kinases in the superfamily; orange, elements are present in more than two, but not all, of the kinases in the superfamily; red, elements shared between only two families; purple, elements seen only in this family, but inserted within in the portion of the chain forming the universal core; blue, elements seen only in this family, and connected to the N- or C-terminal ends of the universal core. Secondary structural elements are labeled according to the standard conventions for the individual structure. As in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a>, the glycine-rich loop is rendered in green and the loop forming the linker region is rendered in red. For clarity, the conserved residues shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-g001" target="_blank">Figure 1</a> are not rendered in these structures, though in most cases they are similar. Structures shown are as follows: (A) aminoglycoside phosphotransferase (APH(3′)-IIIa [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b24" target="_blank">24</a>]); (B) CK (CKA-2 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b23" target="_blank">23</a>]); (C) ChaK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b20" target="_blank">20</a>]; (D) PI3K [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b21" target="_blank">21</a>]; (E) AFK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b22" target="_blank">22</a>]; and (F) PIPKIIβ [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b19" target="_blank">19</a>]. Molecular renderings in this figure were created with MOLSCRIPT [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0010049#pcbi-0010049-b90" target="_blank">90</a>].</p