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1. Introduction
2. Chemical structure representation
3. Atom positions in space (1)
4. Atom positions in space (2)
5. Atom positions in space (3)
6. Redundant connection table
7. Non-redundant connection table
8. Atom numbering
9. MDL/Symyx molfile (.mol) (1)
10. MDL/Symyx molfile (.mol) (2)
11. Protein Data Bank (PDB) format
12. PDB- description of the macromolecule
13. PDB- X-ray diffraction and resolution
14. PDB- primary sequence of amino acids
15. PDB- SS bond information between AA
16. PDB- position information of each atom
17. PDB- connection information
18. Molecule representation extracted from PDB file
19. Daylight SMILES
20. Daylight SMILES- linear molecules
21. Daylight SMILES- branches
22. Daylight SMILES- rings
23. Daylight SMILES- salts and isotope information
24. Daylight SMILES- cubane
25. Daylight SMILES- summary
26. Molecular tree and line notation
27. Molecular tree- spheres
28. Molecular tree- spheres depiction
29. Molecular tree- conversion
30. N atoms leads to N sphere-based line notations
31. A canonical (unique) numbering of the atoms
32. Chemical structure elucidation
33. 13C-NMR spectroscopy
34. 13C-NMR spectroscopy- HOSE
35. 13C-NMR spectroscopy- example
36. HOSE code with corresponding substructure
37. HOSE code with corresponding partial spectrum
38. Spectra prediction and spectra interpretation
39. 13C-NMR spectra interpretation
40. Overlaying substructures
41. InChI (1)
42. InChI (2)
43. MARKUSH structures
44. Problem: format conversion
45. Chemical structures: OO programming (1)
46. Chemical structures: OO programming (2)
47. Unified Modelling Language (UML)
48. Chemical structures: OO programming (3)
49. Molecular tree: OO programming (1)
50. Molecular tree: OO programming (2)
51. Chemistry Development Kit (CDK)

Topics Covered

• Chemical structure representation
• Atom positions in space
• Redundant & Non-redundant connection tables
• Atom numbering
• MDL/Symyx molfile (.mol)
• Protein Data Bank (PDB) format
• Daylight SMILES
• Molecular tree and line notation
• Chemical structure elucidation
• 13C-NMR spectroscopy
• HOSE code
• Spectra prediction and spectra interpretation
• Overlaying substructures
• InChI
• MARKUSH structures
• Format conversion
• OO programming
• Unified Modelling Language (UML)
• Chemistry Development Kit (CDK)

Links

Series:

• Introduction to Cheminformatics

Categories:

• Methods

Talk Citation

Publication History

• Published on October 24, 2011
• Reviewed on April 12, 2022

Financial Disclosures

• Prof. Achim Zielesny has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.