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Navigable Slide Index

1. Introduction
2. Fragment-based ligand design (FBLD)
3. Work one or more fragments into one compound
4. Fragment growing
5. Merging and Linking
6. Fragment based design popularity
7. Arguments against FBLD
8. Success milestones in the past
9. Software landscape
10. 3D approaches
11. CAVEAT: a historical FBLD helper
12. "Scoring" in CAVEAT
13. LUDI program
14. MCSS / Hook program
15. BROOD program
16. SHOP program
17. FieldStere program
18. MOE Linker Pharmacophores
19. FlexNovo
20. Non-3D approaches
21. CATS and DOGS
22. Topomers
23. Feature Trees (FTrees) fragment spaces
24. ReCore
25. Re-scaffolding using vectors
26. Major challenges for such software
27. ReCore indexed searching
28. ReCore results delivery
29. ReCore "3D shredding"
30. ReCore needs at least 2 vectors
31. Optional volumes & shapes
32. Three levels of synthetic accessibility checks
33. Synthetic access checks & user chemistry
34. Avoiding bogus conformations
35. Chemical correctness vs. creativity (1)
36. Chemical correctness vs. creativity (2)
37. ReCore performance in real life
38. ReCore proof of concept
39. Link, merge, grow fragments FBLD with ReCore
40. A striking analogy between FBLD and ReCore
41. Linking / merging examples
42. Fragment linking example -thrombin
43. Fragment linking example -ReCore queries
44. Fragment linking example (1)
45. Fragment linking example (2)
46. Fragment merging
47. Thymidylate synthase- a merging example (1)
48. Thymidylate synthase in 3D
49. Thymidylate synthase- Recore result
50. Thymidylate synthase- a merging example (2)
51. A growing example
52. Growing into a pai-pai interaction pattern
53. ABT-737 in 3D
54. Growing into a pai-pai pattern- ReCore solution
55. ReCore solution in 3D
56. Recap: FBLD software assistance
57. Further resources
58. Recommended further reading
59. Acknowledgements

Topics Covered

• Computational chemistry for fragment replacement, fragment evolution/growing/merging & linking
• Bioisostere replacement
• Software assistance for SAR optimisation for medicinal chemists
• Lead optimisation software

Links

Series:

• Introduction to Cheminformatics

Categories:

• Methods

Talk Citation

Gastreich, M. (2011, June 26). Pragmatic virtual fragment-based ligand design [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 22, 2024, from https://doi.org/10.69645/GAHI4274.
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Publication History

• Published on June 26, 2011

Financial Disclosures

• Dr. Marcus Gastreich has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.