Dr. Peter Kolb

Projects
 
In silico function prediction for enzymes of unknown function
It is attempted to annotate enzymes by identifying the correct substrates via the docking of substrate databases.
 

Publications
 
Peer-reviewed articles
 
[10] Docking screens: right for the right reasons?
P. Kolb, and J. J. Irwin
Curr. Top. Med. Chem. 2009, accepted. [review]
 
[9] Structure-based discovery of β2-adrenergic receptor ligands.
P. Kolb*, D. M. Rosenbaum*, J. J. Irwin, J. Fung, B. K. Kobilka, and B. K. Shoichet
Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6843-6848.
 
[8] Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans: a close relative of Phosphotriesterase in the Amidohydrolase Superfamily.
D. F. Xiang, P. Kolb, A. A. Fedorov, M. M. Meier, E. V. Fedorov, T. T. Nguyen, R. Sterner, S. C. Almo, B. K. Shoichet, and F. M. Raushel
Biochemistry 2009, 48, 2237-2247.
 
[7] A double-headed Cathepsin B inhibitor devoid of warhead.
P. Schenker, P. Alfarano, P. Kolb, A. Caflisch, and A. Baici
Prot. Sci. 2008, 17, 2145-2155.
 
[6] Structure-based tailoring of compound libraries for high-throughput screening:
Discovery of novel EphB4 kinase inhibitors.
P. Kolb, C. Berset Kipouros, D. Huang, and A. Caflisch
Proteins: Struct. Funct. Bioinf. 2008, 73, 11-18.
 
[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.
 
[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.
 
[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.
 
[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.
 
[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.
 
* 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. Shoichet (Eds.) Virtual Screening. CRC Press, 2005, 349-378.
 
Patents
 
Lüthi U., Huang D., Kolb P., Cecchini M., Majeux N., Dey F., Audétat S., Barberis A. & Caflisch A.
Aryl urea compounds as β-secretase inhibitors.
European Patent EP1734039, WPO WO/2006/133588 (2006)
 
Lüthi U., Huang D., Kolb P., Cecchini M., Majeux N., Dey F., Audétat S., Barberis A. & Caflisch A.
Triazine β-secretase inhibitors.
European Patent EP1790345, WPO WO/2007/051333 (2007)
 
Reviewer for
 
Biophysical Chemistry
ChemMedChem
Journal of Computational Chemistry
QSAR & Combinatorial Science
Proteins: Structure, Function, and Bioinformatics