Schedule
From I571_2006_Wiki
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Important Notes
- The class will be held 2.30 - 3.45pm Eastern Time, Mondays and Wednesdays. Note that the three main institutions running this class have difference semester calendars, so check for not be attended by some students. We will make every effort to record all classes for playback.
- Official course dates are
- IUB: AUG 28 - DEC 9, NO CLASS NOV 21-26
- IUPUI: AUG 23 - DEC 11, NO CLASS SEP 4, NOV 22-26
- MICHIGAN: SEP 5 - DEC 13, NO CLASS SEP 4, OCT 16-17, NOV 22-26
- Distance Education students will follow the Bloomington (IUB) calendar.
- Slides and recordings will be posted below where available. To replay a recording, you just need a web browser that is enabled for Macromedia Flash.
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Class Schedule
| Date | Lecturer | Subject |
|---|---|---|
| Aug 28 | David Wild | Introduction to the world of chemical informatics. Overview of the class; defining chemical informatics; chemical and bioinformatics; chemical informatics and the pharmaceutical industry; example applications; a glimpse of the future of chemical informatics. PDF slides PDF 6 slides/page Recording |
| Aug 30 | - | No class |
| Sep 4 | - | No class (Labor Day) |
| Sep 6 | David Wild | Representing 2D structures. Kinds of 2D structure representation; atom lookup and connection tables; graph theory; SMILES; SD files; representation nuances; descriptors. Canonicalizing SMILES; representing reactions; representing generic structures; fingerprints; measuring chemical similarity; XML, CML, InChI and other web-oriented representation systems PDF slides PDF 6 slides/page Recording |
| Sep 11 | Gary Wiggins | Commercial vendors & databases I. Systems for browsing databases (STN, SciFinder Scholar, Crossfire Commander); Commercial databases available (CAS, Beilstein, Cambridge Structural Dataset); Spectral Databases; Open Access issues PPT slides (Recording not available) |
| Sep 13 | Kalpana Shankar | Ethnography of Paper: Implications for Electronic Laboratory Notebooks in Scientific Practice Recording |
| Sep 18 | Gary Wiggins | Commercial vendors & databases II. Product demonstrations Recording |
| Sep 20 | David Wild | 2D chemical database applications. Types of searching; substructure searching with SMARTS; similarity searching with fingerprints; demonstrations of searching systems PDF slides PDF 6 slides/page Recording |
| Sep 25 | David Wild | Advanced 2D descriptors and methods. Kinds of descriptor; “mathematical” and topological indices; biological descriptors and their application in ADME/Tox; biological properties; property prediction software; 2D QSAR; cluster analysis; diversity analysis PDF slides PDF 6 slides/page Recording |
| Sep 27 | Rajarshi Guha | What Do QSAR Models Tell Us and Do the Results Make Sense? Why interpretation of QSAR models is required. Interpretation techniques for linear and non-linear models. Case study of the interpretation of linear regression models. Can we determine whether a QSAR model can be used to predict new data? Approaches to determining model validity PDF slides Recording |
| Oct 2 | David Wild | Representing 3D Structures Sources of 3D information; experimental 3D databases; conformational flexibility; distance matrices; estimation of 3D structure; conformational search and minimization; 3D descriptors and fingerprint; representation of proteins PDF slides PDF 6 slides/page Recording |
| Oct 4 | David Wild | 3D Visualization and Computation History of 3D visualization; free visualization and computation tools; 3D QSAR and models of activity; docking & virtual screening (same slides as Oct 2) Recording |
| Oct 9 | David Wild | Chemical Informatics Software Development I PDF slides PDF 6 slides/page Recording |
| Oct 11 | Ian Watson Eli Lilly | Some things I've learned in chemoinformatics PDF slides PDF 6 slides/page Recording |
| Oct 16 | John Barnard Digital Chemistry | Generic and Markush Searching. NOTE: This is during Michigan study break. Michigan students should replay this class online, if unable to attend. Check this page for a link after the class. PDF slides PDF 6 slides/page Recording |
| Oct 18 | NO CLASS | NO CLASS - instead watch Introductory to Laboratory Informatics and optionally other I617 classes. |
| Oct 23 | Jack Bikker Pfizer | Virtual Screening PDF slides PDF 6 slides/page Recording |
| Oct 25 | Rajarshi Guha | Emerging Web Technologies for Chemical Informatics What technologies and tools are available, how they can be used to extend traditional applications and enhance chemical data PDF slides Recording |
| Oct 30 | David Wild | Chemical Informatics Software Development II (same slides as Oct 9) Recording |
| Nov 1 | David Wild | Chemical Informatics Software Development III (same slides as Oct 9) Recording |
| Nov 6 | David Wild | Using OpenEye software for desktop molecular modeling (no slides) Recording |
| Nov 8 | Tom Doman Eli Lilly | Hot Topics in Chemoinformatics PDF slides PDF 6 slides/page Recording |
| Nov 13 | Chihae Yang Leadscope | Using Leadscope for computational drug discovery PDF slides Leadscope Tutorial Recording |
| Nov 15 | Chihae Yang Leadscope | Computational Toxicology PDF slides PDF 6 slides/page Recording |
| Nov 20 | Gary Wiggins | Topic to be announced |
| Nov 22 | - | No class (Thanksgiving) |
| Nov 27 | David Wild | Chemical Informatics Research PDF slides PDF 6 slides/page Recording |
| Nov 29 | David Wild | Chemoinformatics, 'omics', and Systems Biology PDF slides PDF 6 slides/page Recording |
| Dec 4 | Sean Ekins ACT LLC | Systems ADME/Tox PowerPoint slides |
| Dec 6 |
