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ICEP: Indiana Cheminformatics Education Portal
Pages and Files
2D chemical database searching systems
3D visualization, alignment, docking and scoring
Characterizing 2D structures with descriptors and fingerprints
Chemical structures on the web and in the scholarly literature
Cluster Analysis and Diversity Analysis
Data mining of chemical & biological information
MOOCs and Learning Materials Relevant to Cheminformatics
Quantitative Structure-Activity Relationships (QSAR) and Predictive Models
Representation and characterization of 3D structures
Representation of 2D structures on computer
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From a discussion by the Editorial Board of the Journal of Cheminformatics, we decided a special issue of the Journal dedicated to education would be highly desirable. In particular, papers would (i) describe both the history and state of the art in different areas of cheminformatics, with the emphasis on being a practical guide, especially for people outside the field and (ii) show how freely available / open source / "libre" algorithms, tools, and resources can be used for cheminformatics
- chemical identity (descriptors) / Johnny, Christoph / CDK, Mold2 (
- chemical similarity; virtual screening / Peter, Jurgen / ChemAxon, OE, PubChem, Chemspider
- pharmacophores / Yvonnne / ChemAxon (?)
- Clustering; machine learning / Bob C, Curt, ?? / Weka, Orange
- cheminformatics toolkits (CDK, Bioclipse, KNIME, ...) / Egon Willighagen?
- QSAR / Alex / ChemBench, OCHEM
- Property prediction / Bobby, Jonathan/ ACDLabs, ChemAxon
- Cheminformatics, Networks and the Semantic Web / David, Rajarshi, Tony / Chemspider, Chem2Bio2RDF, ChemProt
Resources that could provide useful base material
all can feel free to add papers and contribute to the discussion for each paper
Best practises for chemical structure registration and searching in relational databases
Proposed by Chris Steinbeck, is ready for submission
Cheminformatics, Networks and the Semantic Web
Proposed by David Wild. Describing developments in data integration with the semantic web, and how the resulting networks of data can be used
Article(s) covering open source tools: (I (Michael Berthold) favor variant B, to be honest)
Variant A: Open Source Cheminformatics Tools and Toolkits
Proposed by Michael Berthold. This version would attempt to cover all software out there (and needs lots of co-authors, obviously!)
Variant B1: KNIME Integrating Cheminformatics Toolkits
Proposed by Michael Berthold. This version would focus on KNIME and the cheminformatics tools it integrates.
Variant Bx: ToolX Integrating Cheminformatics Toolkits
Written by others. Bioclipse, Taverna, Orange, ... come to mind?
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