Updated: 11 November 2004

Included in the table below are links to lecture notes or outlines covering the C371 lessons. In addition, there may be a link on the schedule to supplementary material on the Internet (SIRCh or others) that is relevant to a given topic. SIRCh (Selected Internet Resources for Chemistry) contains links to factual sources on the Web where you can get answers to questions you might have.

C371 Schedule Fall 2004
Mondays, 4:40-5:30 PM, CH A400 (IUB); ES 2101 (IUPUI)


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
IUPUI Holiday
"Nomenclature Lite:" A Guide to Naming and Indexing Chemical Compounds Instructor:  Dr. Charles H. Davis
Chemical Nomenclature

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
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:

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

12/6 Meeting to Discuss Projects/Papers

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
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


EndNote and Other Citation Manager Software [SIRCh] Exercise. Importing to EndNote

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