@misc{BujotzekSchuettNielsenetal.2013, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {Efficient Conformational Analysis by Partition-of-Unity Coupling}, journal = {Math Chem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42570}, year = {2013}, abstract = {Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.}, language = {en} } @article{KlimmBujotzekWeber2011, author = {Klimm, Martina and Bujotzek, Alexander and Weber, Marcus}, title = {Direct Reweighting Strategies in Conformation Dynamics}, volume = {65(2)}, journal = {MATCH Commun. Math. Comp. Chem.}, pages = {333 -- 346}, year = {2011}, language = {en} } @article{ScheibeBujotzekDerneddeetal.2011, author = {Scheibe, Ch. and Bujotzek, Alexander and Dernedde, Jens and Weber, Marcus and Seitz, O.}, title = {DNA-programmed spatial screening of carbohydrate-lectin interactions}, volume = {2}, journal = {Chem. Sci.}, pages = {770 -- 775}, year = {2011}, language = {en} } @article{WeberBujotzekAndraeetal.2011, author = {Weber, Marcus and Bujotzek, Alexander and Andrae, Karsten and Weinhart, M. and Haag, Rainer}, title = {Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces}, journal = {J. Mol. Sim.}, year = {2011}, 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} } @inproceedings{FackeldeyBujotzekWeber2012, author = {Fackeldey, Konstantin and Bujotzek, Alexander and Weber, Marcus}, title = {A meshless discretization method for Markov state models applied to explicit water peptide folding simulations}, volume = {89}, booktitle = {Meshfree Methods for Partial Differential Equations VI}, publisher = {Springer}, pages = {141 -- 154}, year = {2012}, language = {en} } @misc{KellermannWeberBujotzek2007, author = {Kellermann, R. and Weber, Marcus and Bujotzek, Alexander}, title = {Vom Dietrich zum Sicherheitsschl{\"u}ssel - Mathematiker des Matheon simulieren neuen Wirkstoff f{\"u}r die Diabetes-Behandlung}, number = {2}, publisher = {DFG-Forschungszentrum Matheon}, year = {2007}, language = {en} } @article{BujotzekWeber2009, author = {Bujotzek, Alexander and Weber, Marcus}, title = {Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach}, volume = {7(5)}, journal = {Journal of Bioinformatics and Computational Biology}, pages = {811 -- 831}, year = {2009}, language = {en} } @article{AbendrothBujotzekShanetal.2011, author = {Abendroth, Frank and Bujotzek, Alexander and Shan, Min and Haag, Rainer and Weber, Marcus and Seitz, Oliver}, title = {DNA-controlled bivalent presentation of ligands for the estrogen receptor}, journal = {Angew. Chem. Int. Ed.}, year = {2011}, language = {en} } @article{BujotzekShanHaagetal.2011, author = {Bujotzek, Alexander and Shan, Min and Haag, Rainer and Weber, Marcus}, title = {Towards a rational spacer design for bivalent inhibition of estrogen receptor}, volume = {25(3)}, journal = {J. Comput.-Aided Mol. Des.}, pages = {253 -- 262}, year = {2011}, language = {en} }