Zu Hauptinhalt springen
Startseite UR


Biochemistry II
Prof. Dr. Rainer Merkl


Our Scientific Goals

We utilize, design, and implement algorithms solving problems of computational molecular biology. More specifically, our goal is to contribute to a deeper understanding of proteins observed in nature. This is why we concentrate on two problems, which are rational protein design and enzyme evolution.   

Protein Design

For rational protein design, we use state-of-the-art software suites like Rosetta, comprehensive databases like InterPro or PDB, and specific algorithms, which we implement if specific tools are not available. Using these methods, we can plan wet-lab experiments together with our collaboration partners.

Enzyme Evolution

We are also interested in elucidating protein evolution by means of phylogenetic methods. To study the evolution of enzymes, we reconstruct the corresponding sequence of predecessors and characterize the properties of the resurrected proteins in collaboration with Prof. Reinhard Sterner and his the group.

Software Development

Our focusing on protein design and evolution is also setting the direction of software design. The tools, which we develop, are often dedicated to the characterization of functionally or structurally important residues. In many cases, we utilize knowledge-based potentials deduced from large data sets like multiple sequence alignments or protein structures to corroborate characteristic properties of proteins or residue-positions. Thus, we deduce properties that can contribute to a classification by means of support vector machines or other state-of-the-art classifiers.

In addition, we analyse large data sets to corroborate the specificity of enzymes or to predict function of so far uncharacterized proteins.

Our webserver offers some of our in silico methods.


Lheizinger 90 90

Leonhard Heizinger

Office: Westliche Naturwissenschaften E3.1.317

Phone: (+49) 941-943-3028
Email: Em Lheizinger

Kheyn 90 90

Dr. Kristina Straub

Office: Westliche Naturwissenschaften E3.1.317

Phone: (+49) 941-943-3028
Email: Straubmail

Rmerkl2014 Bw 90x90

Prof. Dr. Rainer Merkl

Office: Westliche Naturwissenschaften E3.1.319

Phone: (+49) 941-943-3086
Email: Em Rmerkl
Jnazet 90x90

Julian Nazet

Office: Westliche Naturwissenschaften E3.1.317

Phone: (+49) 941-943-3028
Email: Em Jnazet


My team is offering lectures, seminars, and practicals related to computational biology.

This is a link to my courses as detailed by the course catalogue of the University of Regensburg.

All materials can be found at the E-Learning server of the University of Regensburg.

For practicals, we have developed an interactive course (restricted access).

If you are interested in computational biology, this book (written in German)  my be of interest:

R. Merkl, Bioinformatik, Wiley-VCH.


An up-to-date compilation of our publications can be found in several databases. Here are links to our PubMed entries and my ResearchGate and GoogleScholar profiles.


apl. Prof. Dr. Rainer Merkl

University of Regensburg
Department of Biochemistry II
Universitätstraße 31

D-93053 Regensburg

EMAIL: Em Rmerk PHONE: +49-941-943-3086


My office has the room number E3.1.319 and is located in building WNE3.

Campus English Rm1 Small 1

See also this map.

  1. Fakultät für Biologie und Vorklinische Medizin
  2. Faculty Research

Computational Protein Design and Evolution

Group of
adj. Prof. Dr. R. Merkl



Rm Animated

We are interested in understanding the function of proteins by utilizing in silico methods. Often, it is helpful to project additional data onto the 3D structure of a protein.