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Roman Laskowski

Ligand binding sites. Roman Laskowski. Representations of protein ligand-binding sites. Surface coloured by residue conservation. Clefts. Clefts in surface. Visualization of binding-site properties. Visualization of binding-site properties. Depictions of pharmacophores. H-bond acceptors.

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Roman Laskowski

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  1. Ligand binding sites Roman Laskowski

  2. Representations of protein ligand-binding sites

  3. Surface coloured by residue conservation Clefts

  4. Clefts in surface

  5. Visualization of binding-site properties

  6. Visualization of binding-site properties

  7. Depictions of pharmacophores H-bond acceptors Hydrophobic Aromatic H-bond donors

  8. AutoLigand:  A ligand site finder

  9. Representations of protein ligand-binding sites

  10. Protein-ligand interactions

  11. 3tmn – thermolysin + Val-Trp LIGPLOT protein-ligand schematic diagrams

  12. LIGPLOT schematic diagrams

  13. LIGPLOT schematic diagrams

  14. LIGPLOT schematic diagrams

  15. LIGPLOT schematic diagrams

  16. Protein-ligand interaction diagrams PoseView LIGPLOT MOE AstexViewer

  17. Comparing binding of different ligands to same protein 1err 1qku (raloxifene) (estradiol ) Human estrogen receptor

  18. Allosteric site Somewhere else Catalytic site Ligand clusters What ligands bind to a given protein?

  19. Ligand clusters Link

  20. Protein-ligand matrix PHA-739358 PD173955 PD180970 Imatinib Molecular similarity Abl-1 100% 90% 80% 70% 60% 50% 40% C-kit 30% aurora-2 Abl-1 Sequence identity

  21. STITCH: protein-drug interaction networks

  22. PDB structures containing bound drug molecules

  23. Drug data (from DrugBank)

  24. Map to corresponding protein drug targets

  25. Pfam domain architectures

  26. Other structures of the same protein

  27. Dynamic graphs of related Pfam domain architectures

  28. 2jz3: NMR structure of fragment SH2 domain and SOCS box domain Other structures in PDB: Dynamic graphs of related Pfam domain architectures Suppressor of cytokine signaling 3 (mouse)

  29. ArchSchema graphs Each node shows the Pfam domain architecture: Can add UniProt seqs as satellite nodes:

  30. ArchSchema graphs

  31. Indicate 3D coverage: Can add PDB structures: Addition of 3D structural info

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