Epernicus: Peter Kolb, Ph.D.

Peter Kolb, Ph.D.

Position:
Post Doctoral Fellow

Pharmaceutical Chemistry

University of California, San Francisco (San Francisco, CA)
Advisor:
Brian K Shoichet
Degrees:

Ph.D., Biochemistry, University of Zurich (Zurich, Switzerland)

M.Sc., Biochemistry, Theoretical Chemistry, University of Vienna (Vienna, Austria)
Past Advisors:

Amedeo Caflisch (as Post Doctoral Fellow)

Amedeo Caflisch (as Graduate Student - Ph.D.)

Margit Sara (as Graduate Student - Masters)
Research:
Investigation of all aspects of small molecule-protein interactions.
Other Experience:
2007 Consultant, Oncalis AG
Honors:
2007-2009 SNF Fellowship for Prospective Researchers

2005 Coalesix Academic Excellence Award

1998 Performance scholarship awarded by the Faculty for Sciences and Mathematics

1996 Performance scholarship awarded by the Senate of the University of Vienna

Communities:

Peter Kolb's Genealogy

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Peter Kolb's Publications (14)

Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase .
Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Federov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM

Biochemistry. 2010 Jan 26;49(3):611-22
The Hunt for 8-Oxoguanine Deaminase.
Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM

Journal of the American Chemical Society. 2010 Jan 20
Docking and chemoinformatic screens for new ligands and targets.
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK

Current opinion in biotechnology. 2009 Aug;20(4):429-36
Structure-based discovery of beta2-adrenergic receptor ligands.
Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK

Proceedings of the National Academy of Sciences of the United States of America. 2009 Apr 21;106(16):6843-8
Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily.
Xiang D, Kolb P, Fedorov A, Meier M, Federov E, Nguyen T, Sterner R, Almo S, Shoichet B, Raushel F

Biochemistry. 2009 Mar 17;48(10):2237-47
Docking screens: right for the right reasons?
Kolb P, Irwi JJ

Current topics in medicinal chemistry. 2009;9(9):755-70
A double-headed cathepsin B inhibitor devoid of warhead.
Schenker P, Alfarano P, Kolb P, Caflisch A, Baici A

Protein science : a publication of the Protein Society. 2008 Dec;17(12):2145-55
Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors.
Kolb P, Kipouros CB, Huang D, Caflisch A

Proteins. 2008 Oct;73(1):11-8
Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model.
Kolb P, Huang D, Dey F, Caflisch A

Journal of medicinal chemistry. 2008 Mar 13;51(5):1179-88
Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.
Kolb P, Caflisch A

Journal of medicinal chemistry. 2006 Dec 14;49(25):7384-92
In silico discovery of beta-secretase inhibitors.
Huang D, Lüthi U, Kolb P, Cecchini M, Barberis A, Caflisch A

Journal of the American Chemical Society. 2006 Apr 26;128(16):5436-43
Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations.
Huang D, Lüthi U, Kolb P, Edler K, Cecchini M, Audetat S, Barberis A, Caflisch A

Journal of medicinal chemistry. 2005 Aug 11;48(16):5108-11
Fragment-based high-throughput docking.
Peter Kolb, Marco Cecchini, Danzhi Huang, Amedeo Caflisch

In: Juan Alvarez and Brian K. Shoichet (Eds.) Virtual Screening. CRC Press. 2005:349-378
Automated docking of highly flexible ligands by genetic algorithms: a critical assessment.
Cecchini M, Kolb P, Majeux N, Caflisch A

Journal of computational chemistry. 2004 Feb;25(3):412-22

Peter Kolb's Posters and Presentations (9)

Structure-based discovery of β2-adrenergic receptor ligands (presentation)
Peter Kolb

Gorfe Lab, The University of Texas Medical School at Houston; 08/2009
Structure-based discovery of β2-adrenergic receptor ligands (poster)
Peter Kolb, Daniel M. Rosenbaum, John J. Irwin, Juan Jose Fung, Brian K. Kobilka, and Brian K. Shoichet

GRC CADD 2009; 07/2009

Attachment: kolb.grc.cadd2009.pdf
Structure based drug design and LIE models for GPCRs (presentation)
Peter Kolb, Daniel M. Rosenbaum, Anne Marie Jorgensen, John J. Irwin, Brian K Shoichet, and Brian K. Kobilka

ACS 237th National Meeting; 03/2009
Investigating small molecule-protein interactions with docking - applications to drug design and the prediction of enzyme function (presentation)
Peter Kolb

University of Salzburg, Schwarzenbacher Lab; 10/2008
A transferable linear interaction energy model for kinases: derivation and inhibitor discovery (poster)
Peter Kolb, Danzhi Huang, Fabian Dey, and Amedeo Caflisch

Euro-QSAR 2008; 09/2008
Computer-aided drug design for the β2-adrenergic receptor (presentation)
Peter Kolb, Daniel M. Rosenbaum, John J. Irwin, Brian K. Kobilka, and Brian K. Shoichet

Euro-QSAR 2008; 09/2008
Fragment-based tailoring of compound libraries for high-throughput docking and screening (presentation)
Peter Kolb,Catherine Berset Kipouros, Danzhi Huang, Fabian Dey, and Amedeo Caflisch

ACS 236th National Meeting; 08/2008
Predicting enzyme function by docking high-energy intermediates of potential substrates (presentation)
Peter Kolb, Johannes C. Hermann, Ricardo Marti-Arbona, Eman Ghanem, John J. Irwin, Frank M. Raushel, and Brian K. Shoichet

ACS 236th National Meeting; 08/2008
Fragment-based Docking and Drug Design (presentation)
Peter Kolb

MedChem USA 2007; 10/2007

One Figure

Computational structure-based drug design for the β2-adrenergic receptor.

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