• Representation of Chemical Structures
• 37 min
  1. Basics in cheminformatics: representation of chemical structures 1

  • Dr. Thomas Engel
• 28 min
  2. Basics in cheminformatics: representation of chemical structures 2

  • Dr. Thomas Engel
• 35 min
  3. Chemical file formats and line notations

  • Prof. Achim Zielesny
• Visualization of Chemical Structure
• 17 min
  4. Common types of visualization of chemical structure

  • Prof. Robert M. Hanson
• Basic Algorithms in Cheminformatics
• 40 min
  5. Ring searching and aromaticity detection

  • Prof. Dr. Christoph Steinbeck
• 44 min
  6. Substructure searching, similarity calculations and fingerprints

  • Mr. Mark Rijnbeek
• 36 min
  7. Canonization, Morgan algorithm, equivalence classes

  • Dr. Markus Meringer
• Structure Databases
• 46 min
  8. Storing, searching and dissemination of chemical information

  • Prof. Achim Zielesny
• 42 min
  9. Databases, indices and structure-related queries

  • Dr. Wolf-Dietrich Ihlenfeldt
• Quantitative Structure-Activity/Property Relationships
• 40 min
  10. Overview of descriptors

  • Dr. Jörg Kurt Wegner
• Machine Learning in Cheminformatics
• 44 min
  11. Introduction to machine learning and its application in chemistry

  • Dr. Nikolas Fechner
• Cheminformatics in Drug Discovery
• 38 min
  12. Virtual screening

  • Dr. John H. Van Drie
• 47 min
  13. Pharmacophore methods in drug discovery

  • Dr. John H. Van Drie
• 65 min
  14. Pragmatic virtual fragment-based ligand design

  • Dr. Marcus Gastreich
• 44 min
  15. Chemogenomics

  • Dr. John P. Overington
• Molecular Modelling
• 62 min
  16. Molecular modelling: empirical methods

  • Prof. Tim Clark
• 59 min
  17. Molecular modelling: electronic structure methods

  • Prof. Tim Clark
• Computer-Assisted Structure Elucidation
• 53 min
  18. Methods for NMR-spectrum prediction

  • Dr. Wolfgang Robien
• 44 min
  19. Cyber-based structure elucidation

  • Prof. Morton E. Munk
• The Chemical Semantic Web
• 41 min
  20. Semantic chemistry: an overview

  • Dr. Nico Adams
• Open Notebook Science and the Open Access Movement in Chemistry
• 34 min
  21. Open research: motivation, theory, and practice

  • Dr. Cameron Neylon
• Archived Lectures *These may not cover the latest advances in the field
• 48 min
  22. Representation of chemical structures

  • Dr. Thomas Engel

Printable Handouts

PDF

Navigable Slide Index

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.