Open Discussion Forum for Cheminformatics Research


This wiki serves as an open discussion forum for cheminformatics research and related areas (e.g., bioinformatics, semantic web, etc). We hold bi-weekly seminar at Lindley Hall, room 325 and use Skype for remote discussion. The seminar includes two sessions. The first session is an individual talk which lasts about half an hour. One person will take 20 mins to talk about one topic, which includes but not limited to your or other research work and one specific paper. The remaining time will be used for free discussion about recent published papers, interesting blog posts or news and any other topics you think worthy sharing with us. Every seminar, we will have one volunteer to summarize the discussion and put into wiki. We will also hold special discussions for the emerging interesting areas such as drug repurpose, semantic web, etc. Please feel free to contribute to this wiki or contact Abhik Seal (abseal@umail.iu.edu) if you have any questions or suggestions.

Seminars


Backgound papers


Journals


Journal of Chemical Information and Modeling: One of the most popular journals in cheminformatics so far, focusing on chemical information systems, computational modeling and software review.
Journal of Cheminformatics: It covers all cheminformatics areas in general but focuses on open access.
Journal of Molecular Graphics & Modeling: It investigates molecular structure, function, interaction, and design, particular stressing on the molecular modeling.
Journal of Medicinal Chemistry: It concentrates on the study of relationship between molecular structure and biological activity, preferring experiments.
Journal of Computer-Aided Molecular Design: It emphasizes the methods in virtual screening.
Drug Discovery Today: It publishes the opinions or reviews of the novel technologies in current drug discovery process.
BMC Bioinformatics/ Bioinformatics (oxford): More and more cheminformatics (or chemogenomics) works contributing to the bioinformatics community appear in both journals.
Expert Opinion on Drug Discovery: It reviews the novel technologies involved in the drug discovery process, leading to new leads and reduced attrition rates.
Nature Reviews Drug Discovery/Molecular Systems Biology/Nature Chemical Biology/Nature Computational Biology: Significantly important researches in cheminformatics are often published in these nature journal.
Briefing in Bioinformatics: Review of current state of bioinformatics
PLOS Computational Biology: Occasionally, some interesting studies in chemogenomics and system biology appear in this journal.
Journal of Biomedical Semantics: semantic web in Biomedical domain
BMC Systems Biology This journals publishes papers on the Biological systems at molecular and systematic level, Biological Chem-Biological networks.

Blogs


In the Pipeline (http://www.corante.com/pipeline/index.xml)
Useful Chemistry (http://feeds.feedburner.com/UsefulChemistry)
Tripod Development (http://tripod.nih.gov/?feed=rss2)
The Curious Wavefunction (http://wavefunction.fieldofscience.com/feeds/posts/default)
So much to do, so little time (http://blog.rguha.net/?feed=rss2)
petermr's blog (http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?feed=rss2)
Noel O'Blog (http://feeds2.feedburner.com/baoilleach)
Mining Drug Space (http://miningdrugs.blogspot.com/feeds/posts/default)
MedChemBuzz (http://medchembuzz.wordpress.com/feed/)
Drug Truths (http://johnlamattina.wordpress.com/feed/)
Depth-First (http://feeds2.feedburner.com/Depth-first)
ChemSpider Blog (http://feeds.feedburner.com/ChemspiderBlog)
Chemistry in silico (http://cheminsilico.blogspot.com/feeds/posts/default)
chem-bla-ics (http://chem-bla-ics.blogspot.com/feeds/posts/default)
ChEMBL Blog (http://chembl.blogspot.com/)
Fragment Based Drug Discovery(http://fbdd-lit.blogspot.com/)
Practical Fragments (http://practicalfragments.blogspot.in)
Asad's Blog (http://chembioinfo.com/)

News

http://www.genengnews.com/
http://www.sciencedaily.com/articles/health_medicine/


Research Groups

Alexander Tropsha at UNC
Andreas Bender at Cambridge University
Andrew l. Hopkins at University of Dundee
Brian Shoichet at UCSF
David Wild at Indiana University
John P Overington at EBI
Paul Clemons at Broad Institute
Peer Bork at EMBL
Philip Bourne at University of California, San Diego
Tudor Oprea at University of New Mexico
Yuzong Chen at National University of Singapore

Resources


Free & Open Source Resources useful in Cheminformatics & Chemogenomics
Semantic Web Development Toolsand related Software Tools

Communities


Miscellaneous

iHOP - Information Hyperlinked over Proteins - find PubMed abstracts with drug, gene etc associations to a given gene