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Shoichet Lab University of California San Francisco Mission Bay Campus, QB3 Dept. of Pharmaceutical Chemistry 1700 4th Street, Box 2550 San Francisco, CA 94158-2330, USA tel: ++1 (415) 514-4253 fax: ++1 (415) 514-4260 
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Identifying substrates of amidohydrolases.
Finding inhibitors of GPCRs with DOCK.
I am still developing and maintaining DAIM (Decomposition And Identification of Molecules), a program for fragment generation in the context of fragment-based docking and analysis of molecule libraries. For more information and potential other uses of DAIM see the manual or reference [4]. I am always happy about bug reports, but please consider reading this how-to by Simon Tatham before.
On July 6, 2008, DAIM 5.2 has been released. This version supports Sybyl atom types. To obtain it, please go to the download page.
| Peer-reviewed articles | |
| 2008 | |
| [7] | A double-headed Cathepsin B inhibitor devoid of warhead. Patricia Schenker, Pietro Alfarano, Peter Kolb, Amedeo Caflisch, and Antonio Baici 2008, submitted. |
| [6] | Structure-based tailoring of compound libraries for high-throughput screening:
Discovery of novel EphB4 kinase inhibitors. Peter Kolb, Catherine Berset Kipouros, Danzhi Huang, and Amedeo Caflisch Proteins: Struct. Funct. Bioinf. Apr 02, 2008, DOI: 10.1002/prot.22028. [html] [sup] |
| [5] | Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear
interaction energy model. Peter Kolb†, Danzhi Huang†, Fabian Dey†, and Amedeo Caflisch J. Med. Chem. 2008, 51, 1179-1188. [pdf] [sup] |
| 2006 | |
| [4] | Automatic and efficient decomposition of two-dimensional structures of
small molecules for fragment-based high-throughput docking. Peter Kolb, and Amedeo Caflisch J. Med. Chem. 2006, 49, 7384-7392. [pdf] |
| [3] | In silico discovery of β-secretase inhibitors. Danzhi Huang, Urs Lüthi, Peter Kolb, Marco Cecchini, Alcide Barberis, and Amedeo Caflisch J. Am. Chem. Soc. 2006, 128, 5436-5443. [pdf] [sup] |
| 2005 | |
| [2] | Discovery of cell-permeable nonpeptide inhibitors of
β-secretase. Danzhi Huang, Urs Lüthi, Peter Kolb, Karin Edler, Marco Cecchini, Stephan Audétat, Alcide Barberis, and Amedeo Caflisch J. Med. Chem. 2005, 48, 5108-5111. [pdf] [sup] |
| 2004 | |
| [1] | Automated docking of highly flexible ligands by genetic algorithms:
A critical assessment. Marco Cecchini, Peter Kolb, Nicolas Majeux, and Amedeo Caflisch J. Comput. Chem. 2004, 25, 412-422. [pdf] |
| † these authors contributed equally. | |
| Book chapters | |
| Fragment-based high-throughput docking. Peter Kolb, Marco Cecchini, Danzhi Huang, and Amedeo Caflisch In: Juan Alvarez and Brian K. Shoichet (Eds.) Virtual Screening. CRC Press, 2005, 349-378. [pdf] |
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| Other scientific contributions |
