kolblab.org

Networks

The Kolb Lab is located at the Department of Pharmaceutical Chemistry at Philipps-Universität Marburg.
We are a member lab of GLUE,
the Priority Program 2363 "Molecular Machine Learning",
SYNMIKRO,
the transregional collaborative research centre 81 (SFB/Transregio81),
and DRUID.
We are also part of ERNEST, the "European Research Network on Signal Transduction".
Together with the Selent and Bouvier labs, we are investigating biased ligands of the 5-HT2A receptor in the context of the ERANET NEURON project PSYBIAS. Funding is provided by the Federal Ministry of Education and Research under grant number 01EW1909.

The lab was deeply involved in COST Action CM1207 "GLISTEN: GPCR-Ligand Interactions, Structures, and Transmembrane Signalling: a European Research Network"
and part of SynChemBio.
The lab started through the generous funding provided within the DFG's Emmy Noether Programme.
	[en][de]

Research interests

Word cloud generated with wordart.com from publication abstracts.

Small molecules are frequently used both in Nature and therapeutically to modulate the activity of the protein they bind to. Yet, many aspects of small-molecule:protein interactions are surprisingly poorly understood. For instance, ligand polypharmacology, i.e. binding to multiple proteins, often comes as a surprise, although it is frequently precisely the reason for a drug's efficacy or its side effects. On the protein side, a point mutation in the binding site, although only a small change, can abolish drug binding, leading to resistance. Thus, it is highly relevant to develop a comprehensive understanding of small-molecule:protein interaction profiles in molecular detail and correlate these profiles with signaling and metabolic pathways. Our main tool is small molecule docking, but we also use chemoinformatic approaches and molecular dynamics. The research spans method development, basic research and applications. Currently the investigations deal with kinases and G protein-coupled receptors (GPCRs).

Lab members

• Alumni & Guests
• Previous lab pictures

Teaching

We are involved in lectures and lab courses in Pharmaceutical Chemistry. Moreover, we accept students in the Chemistry and Pharmacy curricula for internships. Students with a keen interest in computation, chemistry, and biochemistry and their application to pharmaceutical questions are accepted for B.Sc., M.Sc., and Ph.D. theses (see also below, "Joining the lab").

Scubidoo & Pingui

• The Screenable Chemical Universe Based on Intuitive Data OrganizatiOn (J. Chem. Inf. Model. 2015, 55, 1824-1835, [pdf]) is accessible here.
• For automatic extensions of known (fragment-sized) ligands, PINGUI (J. Med. Chem. 2018, 61, 1118-1129, [pdf]) is available.

PrenDB

• Our database cataloging reactions of prenyltransferases and predicting prenylation sites (J. Biol. Chem. 2017, 292, 4003-4021, [pdf]) can be found at this link.

Daim – a program to generate fragments

• We are 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]. We are always happy about bug reports, but please consider reading this how-to by Simon Tatham before.

• On September 7, 2009 DAIM 5.3 has been released. The update contains several improvements and allows more user choices with respect to the bonds that DAIM cuts. Essentially, it is now possible to override all of the default unbreakable bond definitions. To obtain it, please go to the download page.

Joining the Lab

• Doctoral (Ph.D.) student position within SPP 2363 "Molecular Machine Learning" [pdf] (deadline Mar 04, 2022)