Miscellaneous Links and Notes
From Chemical Informatics and Cyberinfrastructure Collaboratory
Notes from David Wild
Updates December 2006:
- Mic Lajiness at Lilly, David and Rajarshi are pursuing a collaborative project based around expanding the PubDock database with docking runs for several hundred proteins, and developing an end-user tool (with Randy Heiland) for browsing this database. This is a concrete IU-Lilly collaboration.
- Gus Rosania, David and Rajarshi will be collaborating on a joint project to apply Michigan's membrane penetration simulations to PubChem compounds using our cyberinfrastructure
- Students in the I571 class have completed projects related to the CICC listed below. Please contact me if interested
- A Chatbot interface to PubChem (David Jiao)
- Implementation of a chemical informatics workflow in LEAD Xbaya (Harini Gopalakrishnan)
- Implementation of a chemical informatics workflow in .NET (Pulan Yu)
- Evaluation of the KNIME workflow tool (Yi Deng)
- Evaluation of the drug-likeness of compounds in PubChem (George Krudy)
Updates November 2006:
- Implementations of one of our workflows in LEAD and .NET are almost complete
- David will be visiting Michigan MACE in early December
- David and Geoffrey met with Jim Caruthers at Purdue, and made plans for his student Bala Krishnamurthy to connect with me, Rajarshi and Jake Kim to (1) implement Oscar3 web service at Purdue as an example of running a local web service behind a firewall and (2) help him build a web service client to search our PubChem database for structures as an example of allowing them to connect to 'the outside world' of our cyberinfrastructure
- Rajarshi has implemented the Michigan PKCell calculator as a web service (see usage notes) and with a web interface.
- Rajarshi has developed some effective Random Forest toxicity models with Scripps
- It looks like we might have a project going in the next few weeks with Eli Lilly (Mic Lajiness) with two areas: connecting to our database web services (pubdock etc) from their Mobius system, and doing HCI with scientists in a confined study. More soon.
- Christine Humbet at Wyeth (my ex boss from Pfizer) is rather interested in what we're doing. She's currently looking at Berthold's Knime workflow tool. I will probably make a trip in December
- Val Gillet at Sheffield is willing to share code with us for us to wrap as web services. She is currently inventorying what she could give us - should have something in the next week or so
- Rajarshi has now made Pubdock and Pub3D, now all available thanks to Marlon in the CICC Gridsphere.
- A paper entitled "Smart Mining of Drug Discovery Information: 1. A web service and workflow infrastructure" has been submitted to the Journal of Chemical Information and Modeling
- We're making good progress on data mining (Wu, Wang, Klingingsmith) and hope to have concrete results in the next month and a publication submitted by January
- I am visiting Phil Hajduk at Abbott Labs in January to help them with chemical informatics education of their chemoinformatics group
More information is on David Wild's wiki
Other Notes
- German Conference on Chemoinformatics open for Registration: http://scholle.oc.uni-kiel.de/users/cic/tagungen/workshop06/Programm_CIC_2006.pdf
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.
Maintained by the Finley Lab, Wayne State University School of Medicine
