Publications


Peer-reviewed articles
2017
36 The allosteric site regulates the voltage sensitivity of muscarinic receptors
Annika Hoppe, Maria Martí-Solano, Matthäus Drabek, Moritz Bünemann, Peter Kolb, Andreas Rinne
Cell Signal. 2017, 42, 114-126. [pdf]
35 Identification and in silico structural analysis of Gallus gallus Protein Arginine Methyltransferase 4 (PRMT4)
Hannah Berberich, Felix Terwesten, Sinja Rakow, Peeyush Sahu, Caroline Bouchard, Sjaak Philipsen, Peter Kolb, Uta-Maria Bauer
FEBS Open Bio 2017, accepted. [pdf]
34 An open source pharma roadmap
Manica Balasegaram, Peter Kolb, John McKew, Jaykumar Menon, Piero Olliaro, Tomasz Sablinski, Zakir Thomas, Matthew H. Todd, Els Torreele, John Wilbanks
PLOS Med 2017, 14, e1002276. [pdf][essay]
33 Similarity- and substructure-based development of β2-adrenergic receptor ligands based on unusual scaffolds
Denis Schmidt, Jakub Gunera, Jillian G. Baker, Peter Kolb
ACS Med. Chem. Lett. 2017, 8, 481-485. [pdf]
32 PrenDB: A Substrate Prediction Database to Enable Biocatalytic Use of Prenyltransferases
Jakub Gunera, Florian Kindinger, Shu-Ming Li, Peter Kolb
J. Biol. Chem. 2017, 292, 4003-4021. [pdf]
2016
31 GPCRdb: The G protein-coupled receptor database - An introduction
Christian Munk, Vignir Isberg, Stefan Mordalski, Kaspar Harpsøe, Krzysztof Rataj, Alexander Hauser, Peter Kolb, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam
Br. J. Pharmacol. 2016, 173, 2195-2207. [pdf][review]
30 Structure-based virtual screening for dopamine D2 receptor ligands as potential antipsychotics
Agnieszka A. Kaczor, Andrea G. Silva, María I. Loza, Peter Kolb, Marián Castro, Antti Poso
ChemMedChem 2016, 11, 718-729. [pdf]
29 Three stories on Eph kinase inhibitors: from in silico discovery to in vivo validation
Andrea Unzue, Karine Lafleur, Hongtao Zhao, Ting Zhou, Jing Dong, Peter Kolb, Johanna Liebl, Stefan Zahler, Amedeo Caflisch, Cristina Nevado
Eur. J. Med. Chem. 2016, 112, 347-366. [pdf][review]
28 Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry
Maria Martí-Solano, Denis Schmidt, Peter Kolb, Jana Selent
Drug Discov. Today 2016, 21, 625-631. [pdf][review]
2015
27 The quorum-sensing regulator ComA from Bacillus subtilis activates transcription using topologically distinct DNA motifs
Diana Wolf, Valentina Rippa, Juan Carlos Mobarec, Patricia Sauer, Lorenz Adlung, Peter Kolb, Ilka Bischofs
Nucleic Acids Res. 2015, 44, 2160-2172. [pdf]
26 The mode of agonist binding to a G protein-coupled receptor switches the effect that voltage changes have on signaling
Andreas Rinne, Juan Carlos Mobarec, Martyn Mahaut-Smith, Peter Kolb, Moritz Bünemann
Sci. Signal. 2015, 8, ra110. [pdf] [podcast]
25 SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability
Florent Chevillard, Peter Kolb
J. Chem. Inf. Model. 2015, 55, 1824-1835. [pdf] F1000 recommendation
24 Fragment-based similarity searching with infinite color space
Jakub Gunera, Peter Kolb
J. Comput. Chem. 2015, 36, 1597-1608. [pdf]
23 Tryptophan C5-, C6- and C7-Prenylating Enzymes Displaying a Preference for C-6 of the Indole Ring in the Presence of Unnatural Dimethylallyl Diphosphate Analogues
Julia Winkelblech, Mike Liebhold, Jakub Gunera, Xiulan Xie, Peter Kolb, Shu-Ming Li
Adv. Synth. Catal. 2015, 357, 975-986. [pdf]
22 Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant
Jie Yin, Juan Carlos Mobarec, Peter Kolb, Daniel M. Rosenbaum
Nature 2015, 519, 247-250. [pdf] [press release] [news item @ derstandard.at] F1000 recommendation
21 Identifying Modulators of CXC Receptors 3 and 4 with Tailored Selectivity using Multi-Target Docking
Denis Schmidt, Viachaslau Bernat, Regine Brox, Nuska Tschammer*, Peter Kolb*
ACS Chem. Biol. 2015, 10, 715-724. [pdf]
2014
20 Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing D-Xylono-1,4-lactone-5-phosphate and L-Arabino-1,4-lactone-5-phosphate
Magdalena Korczynska, Dao Feng Xiang, Zhening Zhang, Chengfu Xu, Tamari Narindoshvili, Siddhesh Kamat, Howard J. Williams, Shawn S. Chang, Peter Kolb, Brandan S. Hillerich, J. Michael Sauder, Stephen K. Burley, Steven C. Almo, Subramanyam Swaminathan, Brian K. Shoichet, and Frank M. Raushel
Biochemistry 2014, 53, 4727-4738. [pdf]
2013
19 Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants
Martin Stieler, Johannes Weber, Martin Hils, Peter Kolb, Andreas Heine, Christian Büchold, Ralf Pasternack, and Gerhard Klebe
Angew. Chem. Int. Ed. 2013, 52, 11930-11934. [pdf]
18 Computergestützte Entwicklung selektiver Liganden G Protein-gekoppelter Rezeptoren.
Denis Schmidt, and Peter Kolb
Dtsch. Med. Wochenschr. 2013, 138, 2260-2264. [pdf] [review]
17 Structural and functional characterization of a phosphatase domain within yeast general transcription factor TFIIIC.
Nicholas M. I. Taylor, Sebastian Glatt, Marco L. Hennrich, Gudrun von Scheven, Helga Grötsch, Carlos Fernández-Tornero, Vladimir Rybin, Anne-Claude Gavin, Peter Kolb, and Christoph W. Müller
J. Biol. Chem. 2013, 288, 15110-15120. [pdf]
2012
16 Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists.
Peter Kolb*, Khai Phan, Zhan-Guo Gao, Adam C. Marko, Andrej Sali, Kenneth A. Jacobson*
PLOS ONE 2012, 7, e49910. [pdf]
15 Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones.
Dao Feng Xiang, Peter Kolb, Alexander A. Fedorov, Chengfu Xu, Elena V. Fedorov, Tamari Narindoshivili, Howard J. Williams, Brian K. Shoichet*, Steven C. Almo*, and Frank M. Raushel*
Biochemistry 2012, 51, 1762-1773. [pdf]
2011
14 The Golden Age of GPCR Structural Biology: Any Impact on Drug Design?
Peter Kolb* and Gerhard Klebe*
Angew. Chem. Int. Ed. 2011, 50, 11573-11575. [comment] [pdf]
2010
13 The hunt for 8-Oxoguanine Deaminase.
Richard S. Hall, Alexander A. Fedorov, Ricardo Marti-Arbona, Elena V. Fedorov, Peter Kolb, J. Michael Sauder, Stephen K. Burley, Brian K. Shoichet, Steven C. Almo and Frank M. Raushel
J. Am. Chem. Soc. 2010, 132, 1762-1763. [pdf] F1000 recommendation
12 Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to Human Renal Dipeptidase.
Jennifer A. Cummings, Tinh T. Nguyen, Alexander A. Fedorov, Peter Kolb, Chengfu Xu, Elena V. Fedorov, Brian K. Shoichet, David P. Barondeau, Steven C. Almo, and Frank M. Raushel
Biochemistry 2010, 49, 611-622. [pdf]
2009
11 Docking & chemoinformatic screens for new ligands and targets.
Peter Kolb, Rafaela S. Ferreira, John J. Irwin, and Brian K. Shoichet
Curr. Op. Biotech. 2009, 20, 429-436. [review] [pdf]
10 Docking screens: right for the right reasons?
Peter Kolb, and John J. Irwin
Curr. Top. Med. Chem. 2009, 9, 755-770. [review] [pdf]
9 Structure-based discovery of β2-adrenergic receptor ligands.
Peter Kolb, Daniel M. Rosenbaum, John J. Irwin, Juan José Fung, Brian K. Kobilka*, and Brian K. Shoichet*
Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6843-6848. [pdf] [sup] [Comment @ Curious Wavefunction]
The x-ray structure of compound 1 described in this paper has been solved by Wacker et al., and our predicted pose corresponds to the crystallographic one within 0.9 Å RMSD!
8 Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans: a close relative of Phosphotriesterase in the Amidohydrolase Superfamily.
Dao Feng Xiang, Peter Kolb, Alexander A. Fedorov, Monika M. Meier, Elena V. Fedorov, Tinh T. Nguyen, Reinhard Sterner*, Steven C. Almo*, Brian K. Shoichet*, and Frank M. Raushel*
Biochemistry 2009, 48, 2237-2247. [pdf] [sup]
2008
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.
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. *co-corresponding authors.
Book chapters
B2 Fragment-based High-throughput Docking and Library Tailoring.
Peter Kolb
In: Rachelle J. Bienstock (Ed.) Library Design, Search Methods and Applications of Fragment-Based Drug Design. ACS Books, 2011, 131-147. [pdf]
B1 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]
Other writings
W2 The 15 things that surprised me most when I started out as an independent group leader.
Peter Kolb, Verena Klappstein, Ralf Tonner
J. Postdoc. Aff. 2012, 2, 30-34. [pdf]
W1 Explicit and implicit barriers to the international mobility of scientists.
Peter Kolb
J. Postdoc. Aff. 2011, 1, 46-48. [pdf]
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