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Former PostDoc (until June 2007) Group of Prof. Dr. Amedeo Caflisch Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland  contact page
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As of September 2007, I have moved to UCSF. Please use the following new address: 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  Please find my current homepage at UCSF here. |
As a first step in our docking program suite, a program for the decomposition of molecules has been developed. This program is called DAIM (Decomposition And Identification of Molecules) and greatly facilitates the use of the in-house programs SEED & FFLD. DAIM is also highly useful outside of the context of our docking suite (fragment generation, library analysis,...). 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.
Another task is to find new optimisers to make FFLD - our program for flexible ligand docking - faster.
Inhibitors against various kinase targets are being searched in libraries of up to 4M compounds.
See reference [5].
| Peer-reviewed articles | |
| [7] | A double-headed Cathepsin B inhibitor devoid of warhead. Patricia Schenker, Pietro Alfarano, Peter Kolb, Amedeo Caflisch, and Antonio Baici Prot. Sci. 2008, 17, 2145-2155. [pdf] [sup] |
| [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. 2008, 73, 11-18. [pdf] [sup] |
| [5] | Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear
interaction energy model. P. Kolb†, D. Huang†, F. Dey†, and A. Caflisch J. Med. Chem. 2008, 51, 1179-1188. [pdf] [sup] |
| [4] | Automatic and efficient decomposition of two-dimensional structures of
small molecules for fragment-based high-throughput docking. P. Kolb, and A. Caflisch J. Med. Chem. 2006, 49, 7384-7392. [pdf] |
| [3] | In silico discovery of β-secretase inhibitors. D. Huang, U. Lüthi, P. Kolb, M. Cecchini, A. Barberis, and A. Caflisch J. Am. Chem. Soc. 2006, 128, 5436-5443. [pdf] [sup] |
| [2] | Discovery of cell-permeable nonpeptide inhibitors of
β-secretase. D. Huang, U. Lüthi, P. Kolb, K. Edler, M. Cecchini, S. Audétat, A. Barberis, and A. Caflisch J. Med. Chem. 2005, 48, 5108-5111. [pdf] [sup] |
| [1] | Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. M. Cecchini, P. Kolb, N. Majeux, and A. Caflisch J. Comput. Chem. 2004, 25, 412-422. [pdf] |
| † these authors contributed equally. | |
| Book chapters | |
| Fragment-based high-throughput docking. P. Kolb, M. Cecchini, D. Huang, and A. Caflisch In: J. Alvarez and B. K. Shoichet (Eds.) Virtual Screening. CRC Press, 2005, 349-378. |
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| Other scientific contributions |