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Cheminformatics

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Cheminformatics

This course is sponsored by the ACS Division of Chemical Education's Committee on Computers in Chemical Education. This course is designed for either graduate students, or upper division undergraduate students. In this course students will lean how molecules are represented on computers, and use PubChem and a variety of open source software to learn some basic coding and to access and analyze data obtained through a variety of APIs.

Chemistry
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Mục lục· 80 mục
  1. 01: Introduction
  2. 1.01: Introduction
  3. 1.02: Brief History of Cheminformatics
  4. 1.03: Introduction to Data and Databases
  5. 1.04: Installing Python
  6. 1.05: Installing R
  7. 1.06: Installing Mathematica
  8. 1.07: Accessing PubChem through a Web Interface
  9. 1.08: Programmatic Access to the PubChem Database
  10. 1.09: Cheminformatics Resources
  11. 1.10: Python Assignment 1
  12. 1.11: R Assignment 1
  13. 1.12: Mathematica Assignment 1
  14. 02: Representing Small Molecules on Computers
  15. 2.01: Introduction
  16. 2.02: Connection Tables
  17. 2.03: Molecular Graph Issues
  18. 2.04: Line Notation
  19. 2.05: Structural Data Files
  20. 2.06: Chemical Resolvers Molecular Editors and Visualization
  21. 2.07: Python Assignment
  22. 2.7.01: Python Assignment 2A
  23. 2.7.02: Python Assignment 2B
  24. 2.08: R Assignment
  25. 2.8.01: R Assignment 2A
  26. 2.8.02: R Assignment 2B
  27. 2.09: Mathematica Assignment
  28. 2.9.01: Mathematica Assignment 2A
  29. 2.9.02: Mathematica Assignment 2B
  30. 03: Database Resources in Cheminformatics
  31. 3.01: Database Basics
  32. 3.02: Database Management
  33. 3.03: Public Chemical Databases
  34. 3.04: Data Organization in PubChem as a Data Aggregator
  35. 3.05: Database Query Introduction
  36. 3.06: Special Notes on Using Public Chemical Databases
  37. 3.07: Mathematica Assignment
  38. 3.08: Python Assignment
  39. 3.09: R Assignment
  40. 3.10: R Assignment (binder test)
  41. 3.11: Assignments
  42. 04: Searching Databases for Chemical Information
  43. 4.01: PubChem Web Interfaces for Text
  44. 4.02: Text Search in PubChem
  45. 4.03: Additional Data Retrieval Approaches in PubChem
  46. 4.04: Searching PubChem Using a Non-Textual Query
  47. 4.05: Programming Topics
  48. 4.06: Python Assignments
  49. 4.07: R Assignment
  50. 4.08: Mathematica Assignment
  51. 05: 5. Quantitative Structure Property Relationships
  52. 5.01: Quantitative Structure-Property Relationships
  53. 5.02: Similar-Structure Similar-Property Principle
  54. 5.03: Molecular Descriptors
  55. 5.3.01: Exercise 5.1 solution
  56. 5.3.02: Exercise 5.2 solution
  57. 5.04: Mathematica Assignment
  58. 5.05: Python Assignment
  59. 5.06: R Assignment
  60. 06: Molecular Similarity
  61. 6.01: Molecular Descriptors
  62. 6.02: Similarity Coefficients
  63. 6.03: Discussion
  64. 6.04: Python Assignment
  65. 6.05: R Assignment
  66. 6.06: Mathematica Assignment
  67. 07: Computer-Aided Drug Discovery and Design
  68. 7.01: Reading
  69. 7.02: Mathematica Assignment
  70. 7.03: Python Assignment-Virtual Screening
  71. 7.04: R Assignment
  72. 7.05: Molecular Docking Experiments
  73. 08: Machine-learning Basics
  74. 8.01: Machine Learning Basics
  75. 8.02: Mathematica Assignment
  76. 8.03: Python Assignment
  77. 9.01: Programming Operators
  78. 9.02: Jupyter Notebooks Tutorial
  79. 9.03: Introduction to Mathematica
  80. 9.04: Python