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From I571/ChE531 2007 Class Wiki
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[edit] Welcome to I571 / ChE531
Welcome to the 2007 I571 / ChE531 Wiki Page. This will be the main repository for information about the I571 Chemical Information Technology course (ChE531 Introduction to Chemoinformatics at Michigan). The course is being taught in parallel at Indiana University Bloomington, IUPUI in Indianapolis, the University of Michigan and to distance education students, using videoconferencing and web conferencing technologies (see picture at Michigan). For more information about the course, contact David Wild, djwild @ indiana.edu, Tel. 812-856-1848. David will also be assisted by Xiao Dong, xdong @ indiana.edu
Consult the User's Guide for information on using the wiki software.
All classes meet at 2.30pm Mondays and Wednesdays in Informatics I105. As we will be using some online videos and learning materials, the class will not meet every time. Please see the schedule for more details.
Here is a draft Syllabus for the class.
[edit] Connection information for Distance Students
- From your phone, dial 1-800-940-6112, and enter the passcode
- Go to http://breeze.iu.edu/cheminfo1 and log in as a guest
- If you have any accessing problems during the class, try sending a chat message in Breeze. If that doesn't work, interrupt the teleconference, or call David's cellphone (number will be given out in email)
[edit] Class Schedule
| Date | Lecturer | Subject | Links |
|---|---|---|---|
| Aug 27 | David Wild | Introduction to the class and the world of cheminformatics | Slides (PDF) Homework Aug 27 Recording |
| Aug 29 | David Wild | Representing 2D structures on computer | Booklet Slides (PDF) Recording |
| Sep 3 | David Wild | NO CLASS (LABOR DAY) | - |
| Sep 5 | David Wild | 2D Chemical database theory | Slides (PDF) Homework - Assignment 1 Recording |
| Sep 10 | David Wild | 2D Chemical database searching systems | Slides same as Sep 5 SMARTS Depict PostgreSQL notes Recording |
| Sep 12 | David Wild | Techniques that use 2D structures | Slides (PDF) Recording |
| Sep 17 | David Wild | 3D representation, visualization and computation | Slides (PDF) Recording |
| Sep 19 | David Wild | Continuing 2D and 3D methods | Homework - Assignment 2 Recording |
| Sep 24 | Rajarshi Guha | Integrating R with the CDK for QSAR modeling | Slides (PDF) Recording |
| Sep 26 | David Wild | Practical application of techniques | PracticalDocking Recent Docking Paper Recording |
| Oct 1 | Brian Winterman & Roger Beckman | Chemical Information Sources | Slides Software download CIS List Recording |
| Oct 3 | David Wild | Machine Learning and Cheminformatics | Machine Learning Notes |
| Oct 8 | Ian Watson | Some Practical Lessons Learned in the Pharmaceutical Industry | Slides (PDF) Recording |
| Oct 10 | David Wild | Developing Cheminformatics Software I | Slides (PDF) Recording |
| Oct 15 | - | CLASS CANCELLED | - |
| Oct 17 | David Wild | Developing Cheminformatics Software II | Programming Notes WOPP Recording |
| Oct 22 | David Wild | Developing Cheminformatics Software III | Creation of a Server Environment Recording |
| Oct 24 | David Wild | Midterm Coffee Break & Paper Discussion | Blog |
| Oct 29 | Kalpana Shankar | The ethnography of paper | Slides (PDF) Recording |
| Oct 31 | David Wild | Web 2.0, Semantic Web and Cheminformatics | Web 2.0 and Mashups Semantic Web 1 Semantic Web 2 Web 2.0 / SW Links Recording |
| Nov 5 | David Wild | Web 2.0, Semantic Web and Cheminformatics continued | Semantic Web Web Services Dublin Core Recording |
| Nov 7 | David Wild | Online resources for cheminformatics | Chemoinf Recording |
| Nov 12 | Robin Truelove | Workflows and Pipeline Pilot | Recording |
| Nov 14 | - | NO CLASS | Depth First Blog Science Hack videos |
| Nov 19 | Jack Bikker | Virtual Screening | Slides (PDF) [Recording |
| Nov 21 | - | NO CLASS - THANKSGIVING | |
| Nov 26 | Chihae Yang | Data Mining with cheminformatics methods in drug discovery | Slides (PDF) |
| Nov 28 | Chihae Yang | Classification and Modeling | Slides (PDF) |
| Dec 3 | Sean Ekins | Computational Toxicology | Slides (PDF) Recording |
| Dec 5 | John Barnard | Generic and Markush Structures | Slides (PDF) Recording |
[edit] Resources
This section contains a selection of journal articles, web sites and other resources which you are encouraged to look at. Some of these will be used in class homeworks
[edit] Recommended Books
- Computer Applications in Pharmaceutical Research and Development $125 (Wiley, Amazon).
- Introduction to Chemoinformatics $77 (Amazon).
- Chemoinformatics: a textbook $95 (Amazon).
[edit] General background and issues in cheminformatics
- Chemistry Plans a Structural Overhaul, Nature Jobs, 12 Sept 2002 (click for PDF).
- Recent Advances in Chemoinformatics, Journal of Chemical Information and Modeling, 2007, 47, 1279-1293
[edit] Websites
- Cheminformatics at Indiana University
- Blogs: Chem-Bla-Ics - Murray Rust - O'Boyle - Useful Chemistry
[edit] Coursework
Grading for this class will be based on short assignments (50%) and a final project (50%). For the short assingments, please email your submissions directly to xdong @ indiana.edu (copied to djwild @ indiana.edu), with the subject line "I571 assignment (assignment number) for (your name)". Please only put one assignment per email. Assignments will be listed below, with due dates and how much they count toward your grade. See the Main Project page for main project suggestions.
ASSIGNMENT 1 - 10% OF GRADE - DUE FRI, SEP 14
- Figure out 2 possible SMILES for Adamantane. It is good to draw a structure and number it first. Note that Adamantane is not aromatic. You might want to check out the drawing tool at Molinspiration
- Try out your structures on the Daylight Depict Tool
- Try similiarity search yourself at PubChem using one of the Adamantane structures as your query, and a >=90% similarity search.
- Submit: two numbered drawings of Adamantane with associated SMILES (scan of pen drawing OK)[4 marks]; your Daylight depictions for the two structures [3 marks]; the top 3 results of your similarity search on PubChem (pasted screenshot OK) [3 marks].
ASSIGNMENT 2 - 10% OF GRADE - DUE FRI, OCT 5
- Go to PubChem (http://pubchem.ncbi.nlm.nih.gov/) and find five compounds that are kinase inhibitors (you can search for “kinase inhibitor”) and five that are not (any kind of search you like)
- Paste the SMILES for your 10 structures in turn into the Molinspiration bioactivity calculator (http://www.molinspiration.com/cgi-bin/properties) and note the predicted Kinase values
- Plot the values on the curves on ALL the graphs at http://www.molinspiration.com/docu/miscreen/druglikeness.html - you can plot the points on the image of the graphs, using two different colors for real kinase inhibitors and non-inhibitors
- Write a short paragraph describing whether you think the Kinase predictions are good, based on your analysis of the plots on the Kinase and other graphs
- Submit: a list of your 5 inhibitor and 5 non-inhibitor SMILES; graphs with your 10 compounds plotted on for all four graphs; and your short discussion
ASSIGNMENT 3 - 10% OF GRADE - DUE WED, OCT 24
- Pick a recent paper in cheminformatics, preferably one that is related to an area we have covered already. Make sure it hasn't already been reviewed on the Journal Club Blog
- Email me (djwild @ indiana.edu) to check no-one has already picked the paper, and to request blog permissions
- Write a brief synopsis of the paper on the Journal Club Blog
- Prepare a 10-minute discussion of the paper for the Midterm Coffee Break & Paper Discussion on October 24th
ASSIGNMENT 4 - 20% OF GRADE - DUE FRI, DEC 7
- Go Through the ChemVC Drug Design Lesson at http://www.chemvc.com:9160/lesson1/ (you will need a login which I shall supply to each of you)
- Write a short summary of what you have learned about HIV and the use of computational methods in the design of inhibitors (less than 1 page) to me by the due date at djwild @ indiana.edu. If you have suggestions for improvement in the software, please include these at the end of your summary too.