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

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

19. Ligand clusters
Link

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

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

30. ArchSchema
graphs

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