Welcome to ICEP

Remotely teaching Cheminformatics at the University of Michigan

ICEP is a repository of freely accessible cheminformatics educational materials generated by the Indiana University Cheminformatics Program. Given the importance of cheminformatics to 21st century medicine, we at Indiana University emphasize broadening participation in education for cheminformatics and related fields, in particular enabling practitioners in academia, government and industry to learn and apply techniques in this field. In addition to ICEP, we are involved with several other initiatives including: an innovative Distance Education program in Cheminformatics, allowing participation in classes and programs (including M.S. and Ph.D.) by any qualified student with an internet connection and a phone; a Graduate Certificate in Cheminformatics program that allows students to gain a qualification in Cheminformatics through completion of Distance Education courses; the CIC Courseshare Program , allowing cheminformatics courses to be shared with other Big-10 Universities (prototyped with the University of Michigan); and the Journal of Cheminformatics , an open access journal for Cheminformatics. For more information about ICEP or the various courses available at IU contact David Wild .

Introductory cheminformatics learning materials

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The following introductory topics are adapted from materials that we use in our I571 Chemical Information Technology class, which serves as our introductory cheminformatics course at Indiana University. These materials are not meant to replace a good textbook (such as Leach & Gillet or Gasteiger ), but rather to complement these textbooks. All materials are written by David Wild unless otherwise noted. A version of these materials is also kept on David's Cheminformatics & Chemogenomics Blog (click on the Cheminformatics Learning tag) - this latter blog will be kept up-to-date with new materials, journal articles, etc.

• Introducing Cheminformatics
• Representation of 2D structures on computer
• Characterizing 2D structures with descriptors and fingerprints
• 2D chemical database searching systems
• Representing reactions
• Representation and characterization of 3D structures
• Chemical structures on the web and in the scholarly literature
• Cluster Analysis and Diversity Analysis
• Quantitative Structure-Activity Relationships (QSAR) and Predictive Models
• 3D visualization, alignment, docking and scoring
• Data mining of chemical & biological information
• Tools for cheminformatics algorithm development

Resources for setting up educational programs in cheminformatics

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• Curriculum for IU's Graduate Certificate, M.S., and Ph.D. Program
• Challenges for chemoinformatics education in drug discovery. Drug Discovery Today, 11, 9&10 (May 2006), pp436-439
• Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University. Journal of Chemical Information & Modeling 2006; 46(2) pp 495 - 502
• Developing a cheminformatics research and teaching center for the Web 2.0 world (Presentation at April 2008 ACS meeting)
• From Chemical Information to Cheminformatics: Graduate Programs at Indiana University (Presentation at ACS regional meeting, May 2007)
• A Wiki-Based Chemical Information Instructional Resource (Presentation at ACS regional meeting, May 2007)
• Advanced Informatics in Chemistry Education (Bicentennial Conference on Chemical Education, 2008)

News and commentary

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Here are reviews by students and others of recent journal articles and posted on the IU Cheminformatics Journal Club Blog:

IU Chemical Informatics Journal Club

• Mining large heterogenous datasets in drug discovery. Expert Opinion on Drug Discovery. 2009
  Wild, D.J. Mining large heterogenous datasets in drug discovery. Expert Opinion on Drug Discovery. 2009; 4(10), pp 995-1004 “Date mining is defined as the process of identifying valid, novel, potentially us...
• Linguistic feature analysis for protein interaction extraction
  Authors: Timur Fayruzov, Martine De Cock, Chris Cornelis and Veronique Hoste BMC Bioinformatics, 2009 Most text mining approaches rely implicitly or explicitly on linguistic data extracted from text, but only few attempts have been made to...
• Molecular Fingerprint Recombination: Generating Hybrid Fingerprints for Similarity Searching from Different Fingerprint Types
  Author: B. Nisius, J. BajorathSource: ChemMedChem, 2009, 4, 1859 – 1863Even though fingerprints are very popular in similarity searching and a variety of different designs were introduced over the years, the combination of different fingerprints i...
• QSAR and Drug Design
  By David R. BevanThis journal article is about the disciplines like drug design and environmental risk assessment in which QSAR is currently being applied. QSAR attempts to correlate the activities with the structural descriptors / physicochemical...
• STITCH 2: an interaction network database for small molecules and proteins
  Author: Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer and Peer BorkSource: Nucleic Acids Research, 2009, 1–5In this article, the authors present STITCH 2(http://stitch...

Here are the latest news items from IU's Cheminformatics group

Indiana University Cheminformatics News

• Press release - Pfizer grant for chemogenomics research Sep 22, 2010 6:12 pm
  Wednesday, September 22, 2010Last modified: Wednesday, September 22, 2010Pfizer to support Indiana University informatics search for pathways to new medical discoveriesFOR IMMEDIATE RELEASESept. 22, 2010BLOOMINGTON, Ind. -- An Indiana University d...
• Cheminformatics Postdoc wins award for scientific excellence Sep 1, 2010 10:02 am
  Qian Zhu, a postdoctoral fellow working with David Wild, has been named a winner of the fall 2010 CINF Scholarship for Scientific Excellence (see http://acscinf.org/html/sciexcel.html). The scholarship, awarded by the Division of Chemical Informat...
• Chem2Bio2RDF paper in top 10 for BMC Bioinformatics Jun 14, 2010 7:16 am
  The BMC bioinformatics paper is in the top 10 for BMC bioinformatics for the last 30 days, with over 1,000 reads. The paper details our innovative chemogenomics system called Chem2Bio2RDF. You can read the paper here.
• Press Release: IU Cheminformatics and Chemistry Department win funding for potentially high impact collaborative project Apr 13, 2010 8:32 am
  David Wild (as Director of the Chemical Informatics Center) and Amar Flood (Chemistry) have won an IU Collaborative Research and Creative Activity award to bring together some of the latest cheminformatics methods developed at IU with leading-edge...
• Cheminformatics student Bin Chen wins award for scientific excellence Mar 26, 2010 10:03 am
  Indiana Cheminformatics PhD student Bin Chen is a winner of the 2010 CINF Scholarship for Scientific Excellence. The scholarship, awarded by the Division of Chemical Information (CINF) of the American Chemical Society (ACS) was given at the 239th ...

Other resources

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• Cheminformatics Virtual Classroom (ChemVC)
• Python cheminformatics tutorial
• Jobs in cheminformatics: CCL Jobs List