Ruprecht-Karls-Universität Heidelberg

Rebecca Wade
ZMBH Research Group Leader

Im Neuenheimer Feld 282
69120 Heidelberg

Lab located at:
Schloß-Wolfsbrunnenweg 35
69118 Heidelberg, Germany
Tel.: + 49-6221 533 247
Fax: + 49-6221 533 298

Homepage at the Heidelberg Institute for Theoretical Studies

Molecular and Cellular Modeling

Molecular recognition, binding and catalysis are fundamental processes in cell function. The ability to understand how macromolecules interact with their binding partners and participate in complex cellular networks is crucial to prediction of macromolecular function, and to applications such as protein engineering and structure-based drug design.

The Molecular and Cellular Modeling (MCM) group works on the development and application of computer-aided methods to predict and simulate biomolecular interactions. The focus is on proteins and our computational approaches are mostly based on the three-dimensional structures of macromolecules. Techniques cover a wide spectrum from interactive, web-based visualization tools to molecular and Brownian dynamics simulations.

Selected recent publications
Original Papers

Yu, X., Martinez, M., Gable, A.L., Fuller, J.C., Bruce, N.J., Richter, S. and Wade, R.C. webSDA: a web server to simulate macromolecular diffusional association. Nucleic Acids Res., (2015) doi: 10.1093/nar/gkv335.

Salo-Ahen, O.M. H., Tochowicz, A., Pozzi, C., Cardinale, D., Ferrari, S., Boum,Y., Mangani, S., Stroud, R.M., Saxena, P., Myllykallio, H., Costi, M.P., Ponterini, G., and Wade, R.C. Hotspots in an Obligate Homodimeric Anticancer Target. Structural and Functional Effects of Interfacial Mutations in Human Thymidylate Synthase. J. Med. Chem., (2015), 58, 3572–3581. doi: 10.1021/acs.jmedchem.5b00137.

Fuller, J.C., Martinez, M., Henrich, S., Stank, A., Richter, S. and Wade, R.C. LigDig: a web server for querying ligand-protein interactions. Bioinformatics, (2015), 31, 1147-1149, doi:10.1093/bioinformatics/btu784.

Gombos, L., Neuner, A., Berynskyy, M., Fava, L.L., Wade, R.C., Sachse, C., and Schiebel, E. GTP regulates the microtubule nucleation activity of γ-tubulin. Nat Cell Biol., (2013), 15: 1317-27. doi: 10.1038/ncb2863.

Sandikci, A., Gloge, F., Martinez, M., Mayer, M.P., Wade, R., Bukau, B. and Kramer, G. Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat Struct Mol Biol., (2013), 20: 843-50.

Veith, N., Feldman-Salit, A., Cojocaru, V., Henrich,S., Kummer, U. and Wade, R.C. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Comput Biol., (2013), 9: e1003159.

Feldman-Salit, A., Hering, S., Messiha, H.L., Veith, N., Cojocaru, V., Sieg, A., Westerhoff, H.V., Kreikemeyer, B., Wade, R.C., and Fiedler, T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. J Biol Chem., (2013), 288: 21295-306.

Kokh, D.B., Richter, S., Henrich, S., Czodrowski, P., Rippmann, F. and Wade, R.C. TRAPP: a tool for analysis of transient binding pockets in proteins. J Chem Inf Model., (2013), 53: 1235-52.

Balbo, J., Mereghetti, P., Herten, D.-P. and Wade, R.C. The shape of protein crowders is a major determinant of protein diffusion. Biophys. J., (2013), 104: 1576-84.

Oguchi, Y., Kummer, E., Seyffer, F., Berynskyy, M., Anstett, B., Zahn, R., Wade, R.C., Mogk, A. and Bukau, B. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat. Struct. Mol. Biol. (2012), 19, 1338-1346. doi: 10.1038/nsmb.2441.

Brancolini, G., Kokh, D.B., Calzolai, L., Wade, R.C. and Corni, S. Docking of ubiquitin to gold nanoparticles. ACS Nano (2012), 6, 9863-9878. doi: 10.1021/nn303444b.


Yu, X., Cojocaru, V. and Wade, R.C. Conformational diversity and ligand tunnels of mammalian cytochrome P450s. Biotech. Appl. Biochem. (2013) 60, 134-145, doi:10.1002/bab.1074.

Mereghetti, P., Kokh, D., McCammon, J.A. and Wade, R.C. Diffusion and association processes in biological systems: theory, computation and experiment BMC Biophysics (2011) 4:2 doi:10.1186/2046-1682-4-2.

Stein,M., Gabdoulline, R.R. and Wade, R.C. Bridging from molecular simulation to biochemical networks  Curr. Op. Struct. Biol. (2007) 17, 166-172.

A model of the membrane-bound human cytochrome P450 2C9, an enzyme essential for drug metabolism in the human liver (Cojocaru et al., PLoS Comput. Biol., (2011) 7(8):e1002152.).

Snapshot from a Brownian dynamics simulation of fungal surface-active hydrophobin protein molecules diffusing in the presence of a surface (Mereghetti & Wade, BMC Biophysics, (2011) 4:9.).