@article{ReuterFackeldeyWeber2019, author = {Reuter, Bernhard and Fackeldey, Konstantin and Weber, Marcus}, title = {Generalized Markov modeling of nonreversible molecular kinetics}, volume = {17}, journal = {The Journal of Chemical Physics}, number = {150}, doi = {10.1063/1.5064530}, pages = {174103}, year = {2019}, abstract = {Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems.}, language = {en} } @article{ReidelbachWeberImhof2018, author = {Reidelbach, Marco and Weber, Marcus and Imhof, Petra}, title = {Prediction of perturbed proton transfer networks}, volume = {13}, journal = {PLoS ONE}, number = {12}, doi = {https://doi.org/10.1371/journal.pone.0207718}, pages = {e0207718 -- e0207718}, year = {2018}, abstract = {The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80\%, while important network properties are maintained in most predictions.}, language = {en} } @article{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A Square Root Approximation of Transition Rates for a Markov State Model}, volume = {34}, journal = {SIAM. J. Matrix Anal. Appl.}, number = {2}, doi = {10.1137/120899959}, pages = {738 -- 756}, year = {2013}, language = {en} } @article{WeberBujotzekHaag2012, author = {Weber, Marcus and Bujotzek, Alexander and Haag, Rainer}, title = {Quantifying the rebinding effect in multivalent chemical ligand-receptor systems}, volume = {137}, journal = {J. Chem. Phys.}, number = {5}, pages = {054111}, year = {2012}, language = {en} } @article{FastingSchalleyWeberetal.2012, author = {Fasting, Carlo and Schalley, Christoph A. and Weber, Marcus and Seitz, Oliver and Hecht, Stefan and Koksch, Beate and Dernedde, Jens and Graf, Christina and Knapp, Ernst-Walter and Haag, Rainer}, title = {Multivalency as a Chemical Organization and Action Principle}, volume = {51}, journal = {Angew. Chem. Int. Ed.}, number = {42}, pages = {10472 -- 10498}, year = {2012}, language = {en} } @article{SarichDjurdjevacConradBruckneretal.2014, author = {Sarich, Marco and Djurdjevac Conrad, Natasa and Bruckner, Sharon and Conrad, Tim and Sch{\"u}tte, Christof}, title = {Modularity revisited: A novel dynamics-based concept for decomposing complex networks}, volume = {1}, journal = {Journal of Computational Dynamics}, number = {1}, doi = {10.3934/jcd.2014.1.191}, pages = {191 -- 212}, year = {2014}, language = {en} } @article{ErlekamIgdeRoeblitzetal.2019, author = {Erlekam, Franziska and Igde, Sinaida and R{\"o}blitz, Susanna and Hartmann, Laura and Weber, Marcus}, title = {Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC}, volume = {7}, journal = {Computation}, number = {3}, doi = {10.3390/computation7030046}, pages = {46}, year = {2019}, abstract = {In addition to the conventional Isothermal Titration Calorimetry (ITC), kinetic ITC (kinITC) not only gains thermodynamic information, but also kinetic data from a biochemical binding process. Moreover, kinITC gives insights into reactions consisting of two separate kinetic steps, such as protein folding or sequential binding processes. The ITC method alone cannot deliver kinetic parameters, especially not for multivalent bindings. This paper describes how to solve the problem using kinITC and an invariant subspace projection. The algorithm is tested for multivalent systems with different valencies.}, language = {en} } @article{VenkatareddyWilkeErnstetal.2019, author = {Venkatareddy, Narendra Lagumaddepalli and Wilke, Patrick and Ernst, Natalia and Horch, Justus and Weber, Marcus and Dallmann, Andre and B{\"o}rner, Hans G.}, title = {Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces}, volume = {6}, journal = {Advanced Materials Interfaces}, number = {13}, doi = {10.1002/admi.201900501}, pages = {1900501}, year = {2019}, abstract = {Mussel glue-proteins undergo structural transitions at material interfaces to optimize adhesive surface contacts. Those intriguing structure responses are mimicked by a mussel-glue mimetic peptide (HSY*SGWSPY*RSG (Y* = l-Dopa)) that was previously selected by phage-display to adhere to Al2O3 after enzymatic activation. Molecular level insights into the full-length adhesion domain at Al2O3 surfaces are provided by a divergent-convergent analysis, combining nuclear Overhauser enhancement based 2D NOESY and saturation transfer difference NMR analysis of submotifs along with molecular dynamics simulations of the full-length peptide. The peptide is divided into two submotifs, each containing one Dopa "anchor" (Motif-1 and 2). The analysis proves Motif-1 to constitute a dynamic Al2O3 binder and adopting an "M"-structure with multiple surface contacts. Motif-2 binds stronger by two surface contacts, forming a compact "C"-structure. Taking these datasets as constraints enables to predict the structure and propose a binding process model of the full-length peptide adhering to Al2O3.}, language = {en} } @article{KoschekDurmazKrylovaetal.2015, author = {Koschek, and Durmaz, Vedat and Krylova, and Wieczorek, and Gupta, Pooja and Richter, and Bujotzek, Alexander and Fischer, and Haag, Rainer and Freund, and Weber, Marcus and Rademann,}, title = {Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands}, volume = {11}, journal = {Beilstein J. Org. Chem.}, pages = {837 -- 847}, year = {2015}, language = {en} } @article{AbendrothSollederWelkeretal.2015, author = {Abendroth, Frank and Solleder, Marthe and Welker, Pia and Licha, Kai and Weber, Marcus and Seitz, Oliver and Mangoldt, Dorothea}, title = {High affinity flourescence labelled ligands for the estrogen receptor}, volume = {2015}, journal = {Eur. J. Org. Chem.}, number = {10}, pages = {2157 -- 2166}, year = {2015}, language = {en} }