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Welcome
Welcome to the 2006 I571 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. If you would like to try out formatting for the Wiki, you can do so on the Sandbox Page. If you wish, you can create your own page on the Class Members page below. For more information about the course, contact David Wild, djwild@indiana.edu, Tel. 812-856-1848.
Connection information for Distance Students
- From your phone, dial 1-800-940-6112, and enter the passcode 001364#
- 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 Informatics Room I-105 (812-856-2707)
Syllabus, Schedule and Class Recordings
Schedule (including class recordings and slides)
Homework and Coursework
Main Projects
- See Main Projects Page
Short assignments
- Assignment 1 - Introduction
- Read Chemistry Plans a Structural Overhaul
- Check out the JMOL visualizations of docked complexes
- Send me an email (djwild@indiana.edu) to let me know your email address, what you would like to get out of the class and, if possible, your favorite picture of yourself!
- Consider signing up for Bio-IT World or Scientific Computing World
- Assignment 1b - instead of class on August 30... 5% of grade
- Read ONE paper from JCIM and ONE paper from the Sample issue of Drug Discovery Today. Email me a 1 paragraph brief overview of each, then give a couple of comments comparing the flavor of the articles
- 5% of coursework, due by October 1st
- Assignment 2 - 2D representation - 5% of Grade
- Figure out 2 possible SMILES for Adamantane (5% of grade, due Oct 1):
- Try them out on the Daylight Depict Tool
- Good to draw structure & figure out numbers first
- Adamantane is not aromatic
- You might want to check out the drawing tool at Molinspiration
- Figure out 2 possible SMILES for Adamantane (5% of grade, due Oct 1):
- Assignment 5 - Commercial Sources and Database (Gary Wiggins) - 5% of grade, Due Oct 1
- See PDF sheet. Email to wiggins @ indiana.edu and copy to djwild @ indiana.edu
- Assignment 6 - Database Techniques - 5% of grade, Due Oct 1
- Try a substructure and similiarity search yourself at Molinspiration. Note any structures you find particularly surprising on the similarity search. If possible, capture a screenshot of the results (CTRL+PRNT SCRN on PC’s to copy). Email notes and/or screenshots to djwild@indiana.edu (5% of grade)
- Assignment 7 - Advanced 2D methods - 5% of grade, Due Nov 1
- 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
- Do the values fit the curves at http://www.molinspiration.com/docu/miscreen/druglikeness.html ?
- Submit your SMILES and associated values, along with your answer to the above question through email at djwild @ indiana.edu
- Assignment 8 - QSAR - 5% of grade, Due Dec 1
- Email me to ask for a chemvc login, and I will reply with your login details
- Go to ChemVC and click on the QSAR-2D Module link on the left.
- Log on with the username you are supplied with
- Read through the introduction, and follow through all 13 exercise steps, selecting a dataset and parameter values of your choice
- Send me an email with the pasted results from exercise 12, plus any comments or observations about the usefulness of this as a tool for learning about QSAR (was it pleasing/annoying, useful/useless, straightforward/complex to use, etc)?
- Assignment 9 - Leadscope - 10% of grade, Due Dec 1
- Download Leadscope using the instructions given in the email
- Complete the Leadscope Homework (Word document) and email to djwild@indiana.edu
- Assignment 10 - 10 Questions - 10% of grade, Due Dec 8
- Answer the questions in the Assignment 9 document
Coursework and Grading
The course will be graded A-C (with A and B as passing grades), based on short assignments given at the end of classes (50% of grade) and a more substantial main project at the end (40% of the grade). 10% will be awarded for participation in class including homeworks. The main project will include options to suit a variety of tastes and skills (from essay questions to programming assignments).
Recommended Books
- Computer Applications in Pharmaceutical Research and Development $125 (Wiley, Amazon). This will be our main book, and we will be doing class readings from it. If you just get one book, get this one. This is a wide ranging book that goes beyond chemoinformatics, but contextualizes the field extremely well.
- Introduction to Chemoinformatics $77 (Amazon). A seminal introductory book on Chemoinformatics, released a couple of years ago
- Chemoinformatics: a textbook $95 (Amazon). More of a reference book.
- Getting Started in Chemoinformatics Free.
Links and interesting articles
- Chemoinf.com
- Chemical Information Sources
- Daylight DEPICT
- Molecular Connectivity Indices Theory
- Cell Animation (Tom Doman)
- Han Talk on haptic devices (Tom Doman)
- Susan Duncan's Molecular Simulations talk
