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SiteEngine: Functional Sites Structural Search Engine

SiteEngine: Functional Sites Structural Search Engine. Shulman-Peleg A., Nussinov R. and Wolfson H. J. Recognition of Functional Sites in Proteins Structures, J. Mol. Biol. 339(3), 607 633. Complete protein Binding site. 3D transfor-mation. Similarity Score. Input. Output. SiteEngine.

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SiteEngine: Functional Sites Structural Search Engine

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  1. SiteEngine: Functional Sites Structural Search Engine Shulman-Peleg A., Nussinov R. and Wolfson H. J. Recognition of Functional Sites in Proteins Structures, J. Mol. Biol. 339(3), 607 633.

  2. Complete protein • Binding site • 3D transfor-mation. • Similarity Score Input Output SiteEngine SiteEngine • Recognizes surface regions of one proteinthat resemble a specific binding site of another. • Measures the similarity of physico-chemical and geometrical properties.

  3. Biological Motivation • Potential ligands and ligand fragments. • Prediction of side effects. • Inferring a function of a novel protein. • Biological classifications.

  4. 3-D Database Searches Application III: Query: a complete proteinDB: binding sites Application II: Query: a binding site DB: binding sites Application I: Query: a binding site DB: complete proteins DB of complete proteins DB of binding sites

  5. - Hydrogen bond acceptor - Hydrogen bond donor - donor/acceptor - Hydrophobic Aliphatic - Aromatic (PI) contacts Representation III. The solid angle shape function (Connolly 83’) is calculated at the center of each physico-chemical patch. I. Each amino acid is represented by a set of its physico-chemical properties (Schmitt 02’). II. Each property creates a physico-chemical patch on the protein surface.

  6. - cAMP-dependent protein kinase (1atp) - MJ0577 Structural genomics protein (1mjh, ranked 7) Recognition of adenine binding sites • A benchmark data set (121 proteins) was searched for binding sites similar to that of cAMP-dependent protein kinase (1atp). • Ranked 7 was the an ATP binding site of a structurally different “hypothetical” protein MJ0577 from Methanococcus jannaschii. *The ligands are displayed for verification only!

  7. Searching the Entire PDB 1. Searching the ASTRAL dataset with the adenine binding site of c-AMP dependent protein kinase (1atp). Replication factor C (1iqp, purple). Ranked 19. D-Ala-D-Ala ligase (1iow). Ranked 31. 2. Searching the ASTRAL dataset with the estradiol binding site of sex hormone-binding globulin (1lhu). Tropinone reductase (2ae2). Ranked 43. Estrogen sulfotransferase (1aqu). Ranked 38.

  8. Web Server http://bioinfo3d.cs.tau.ac.il/SiteEngine

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