C371 Schedule Fall 2004
Mondays, 4:40-5:30 PM, CH A400 (IUB); ES 2101 (IUPUI)
| DATE |
TOPIC |
SUP. MAT. |
HOMEWORK |
|
0. Introduction to Chemical Informatics
|
|
|
| 8/30 |
Chemoinformatics,
cheminformatics, chemical informatics: What is it?
(PowerPoint by Gary Wiggins)
Chemoinformatics: Where it has come from, where it is now and
where it is going.
(PowerPoint by Peter Willett)
|
Chemical Informatics |
Ex. 1: Join Lists
Due: 9/13 |
9/6;
IUPUI Holiday |
"Nomenclature Lite:" A Guide to Naming and Indexing Chemical Compounds
Instructor: Dr. Charles H. Davis
Chemical Nomenclature
|
[SIRCh]
|
|
|
I. 2D Molecular Structures |
|
|
|
9/13 |
Computer Structure Codes (condensed from John Barnard lectures);
Representation and Manipulation of 2D Molecular Structures
Chemical
Identifiers (Numbers, Formulas, Structures)
|
|
Ex. 2. ChemTK
Due: 9/27 |
| 9/20 |
SMILES 1
|
Tutorial;
JME Applet;
Online SMILES Translator
|
Ex. 3: SMILES
Due: 10/4
|
| 9/27 |
SMILES 2 |
Erlangen/Bethesda Data and Online
Services
|
Ex. 4: SMILES
Due:
10/18
|
|
II. 3D Molecular Structures |
|
|
|
10/4 |
Representation and Manipulation of 3D Molecular Structures
Representing 3D Molecules PowerPoint by David Wild
|
VEGA for 3D structures
|
Ex. 5. Mol Viz/3D
Due: 11/8
|
|
III. Molecular Descriptors
|
|
|
|
10/11 |
Molecular Descriptors
|
|
|
|
IV. Computational Models |
|
|
| 10/25 |
Molecular Modeling Lecture 1 by Dr. Kelsey Forsythe
|
Conformations of Alkylcyclohexanes
|
Ex. 6. Mol. Mod. Assignment
Due: 11/22
|
| 11/1 |
Molecular Modeling Lecture 2 by Dr. Kelsey Forsythe
|
|
|
|
V. Similarity |
|
|
|
10/18 |
Similarity Methods
|
|
|
|
VI. Compound Diversity |
|
|
|
11/8 |
Selecting Diverse Sets of Compounds
Also look at:
http://www.indiana.edu/~cheminfo/C571/c571_Barnard6.ppt
|
|
|
|
VII. High-Throughput Screening (HTS) |
|
|
|
11/15 |
Analysis of High-Throughput Screening Data
|
HTS site
|
|
|
VIII. Virtual Screening |
|
|
|
11/22 |
Virtual Screening
|
Can Informatics Really Save Discovery? (Phil McHale, MDL)
|
|
|
IX. Combinatorial Chemistry |
|
|
|
11/29 |
Combinatorial Chemistry and Library Design
|
CombiChem site
|
|
|
Papers and Projects
Guidelines
|
|
|
| 12/6 |
Meeting to Discuss Projects/Papers |
|
|
12/13;
IUPUI ONLY
|
Meeting to Discuss Projects/Papers |
|
|
| Thursday,
December 16, noon
|
Final Papers or Project Write-ups Due |
|
|
|
Guest Lectures from Previous Semesters |
|
|
| 2003 |
Proteomics at Indiana University
Guest Lecturer: Dr. Randy Arnold |
IU Proteomics Research and Development Facility
|
|
2002;
2001
|
Chemical Data Formats and Standards. - Dr. John C. Bollinger |
Data Standards
|
|
|
Additional Topics of Interest |
|
|
|
Browsers and Chemical MIME |
|
|
|
Browsers and
Chemical MIME
Graphics Formats and File Extensions
|
Daub Networks
|
|
|
Chemical Image
Formats and Viewers
|
Structure/Data Standards;
Plugins & Applets
|
|
|
Chemical Image Formats:
Conversion Programs and
Compression; Chemical Scanners
|
|
|
|
Kinemage; Rasmol and Chime
|
[SIRCh]
|
|
|
Using Excel with Chemical Data |
|
|
|
Importing Beilstein Data Into Excel 1
|
|
|
|
Importing Beilstein Data Into Excel 2
|
|
Exercise Importing Data
|
|
Other Uses of Excel in Chemistry
|
de Levie's Downloadable Resources |
|
|
Metadata; Search Engines; Electronic Journals |
|
|
|
Electronic Journals and Linking;
Search Engines and Metadata
|
|
|
|
Miscellaneous |
|
|
|
EndNote and Other Citation Manager Software
|
[SIRCh]
|
Exercise. Importing to EndNote
|
