Adaptive Spectral Clustering in Molecular Simulation

• Bujotzek, A., & Weber, M. (2009). Efficient simulation of ligand-receptor binding processes using the conformation dynamics approach. Journal of Bioinformatics and Computational Biology, 7(5), 811–831.

  Article  Google Scholar 

• Deuflhard, P., & Weber, M. (2005). Robust perron cluster analysis in conformation dynamics. Linear Algebra and its Applications, 398c, 161–184.

  Google Scholar 

• Haack, F., Röblitz, S., Scharkoi, O., Schmidt, B., & Weber, M. (2010). Adaptive spectral clustering for conformation analysis. ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics, AIP Conference Proceedings, 1281, 1585–1588.

  Google Scholar 

• Klimm, M., Bujotzek, A., & Weber, M. (2011). Direct reweighting strategies in conformation dynamics. MATCH, 65, 333–346.

  MathSciNet  Google Scholar 

• Kube, S., & Weber, M. (2007). A coarse-graining method for the identification of transition rates between molecular conformations. The Journal of Chemical Physics, 126(2), 024103.

  Article  MathSciNet  Google Scholar 

• Röblitz, S. (2008). Statistical error estimation and grid-free hierarchical refinement in conformation dynamics. Doctoral Thesis, FU Berlin.

  Google Scholar 

• von Luxburg, U. (2007). A Tutorial on spectral clustering. Statistics and Computing, 17(4), 395–416.

  Article  MathSciNet  Google Scholar 

• Weber, M. (2006). Meshless methods in conformation dynamics. München: Verlag Dr. Hut. ISBN 3-89963-307-5.

  MATH  Google Scholar 

• Weber, M. (2009). A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator, ZIB Report 09–27, Zuse-Institut Berlin.

  Google Scholar 

• Weber, M., & Andrae, K. (2010). A simple method for the estimation of entropy differences. MATCH Communications in Mathematical and in Computer Chemistry, 63(2), 319–332.

  MathSciNet  Google Scholar 

• Weber, M., & Kube, S. (2008) Preserving the markov property of reduced reversible markov chains. Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, AIP Conference Proceedings, 1048, 593–596.

  Google Scholar 

• Weber, M., Kube, S., Walter L., & Deuflhard, P. (2007). Stable computation of probability densities for metastable dynamical systems. SIAM Journal of Multiscale Modeling and Simulation, 6(2), 396–416.

  Article  MathSciNet  MATH  Google Scholar 

• Weber, M., Rungsarityotin, W., & Schliep, A. (2006). An indicator for the number of clusters using a linear map to simplex structure. In: From Data and Information Analysis to Knowledge Engineering, 29th Annual Conference of the German Classification Society 2005, March 9–11, Studies in Classification, Data Analysis, and Knowledge (pp. 103–110). Heidelberg: Springer.

  Google Scholar 

Download references