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Markov models

Markov models

Markov models

Book chapter

  • B. G. Keller, L. Donati,  S. Aleksić, ”Markov state models in drug design” in "Biomolecular Simulations in Structure-Based Drug Discovery", Wiley-VCH, Weinheim (2019), edited by F.L. Gervasio, V. Spiwok

Markov state models - theory

  • B. G. Keller, J.-H. Prinz,  F. Noé, “Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics,” Chem. Phys., 396, 92–107  (2012) https://doi.org/10.1016/j.chemphys.2011.08.021
  • J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schütte,  F. Noé, “Markov models of molecular kinetics: Generation and validation,” J. Chem.  Phys., 134, 174105 (2011) https://doi.org/10.1063/1.3565032
  • B. Keller, P. Hünenberger,  W. F. van Gunsteren, “An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles,” J. Chem. Theory Comput., 7,  1032–1044 (2011) https://doi.org/10.1021/ct200069c
  • J.-H. Prinz, B. Keller,  F. Noé, “Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables,” Physical Chemistry Chemical Physics, 13, 16912–16927 (2011) https://doi.org/10.1039/C1CP21258C
  • B. Keller, X. Daura,  W. F. van Gunsteren, “Comparing geometric and kinetic cluster algorithms for molecular simulation data,” J. Chem.  Phys. 132, 074110 (2010) https://doi.org/10.1063/1.3301140

Variational Markov models and core-set Markov models

  • L. Martini, B.G. Keller, “Extended Peptide Basis Set for Variational Markov Models: Secondary Structure, Orthonormality, and Undersampled Transitions.” ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.7276859.v1
  • O. Lemke  B. G. Keller, “Density-based cluster algorithms for the identification of core sets,” J. Chem.  Phys., 145, 164104 (2016), https://doi.org/10.1063/1.4965440
  • F. Vitalini, F. Noé,  B. G. Keller, “A Basis Set for Peptides for the Variational Approach to Conformational Kinetics,” J. Chem. Theory Comput., 11,  3992–4004 (2015) https://doi.org/10.1021/acs.jctc.5b00498
  • F. Nüske, B. G. Keller, G. Pérez-Hernández, A. S. J. S. Mey,  F. Noé, “Variational Approach to Molecular Kinetics,” J. Chem. Theory Comput., 10,  1739–1752 (2014) https://doi.org/10.1021/ct4009156

Applications

  • J.-O. Joswig, J. Anders, H. Zhang, C. Rademacher, B.G. Keller “The molecular basis for the pH-dependent calcium affinity of the pattern recognition receptor langerin” J. Biol. Chem (2021) 296 p. 100718. https://doi.org/10.1016/j.jbc.2021.100718
  • J. Witek, S. Wang, B. Schroeder, R. Lingwood, A. Dounas, H.-J. Roth, M. Fouché, M. Blatter, O. Lemke, B. Keller,  S. Riniker, “Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides.,” J. Chem. Inf. Model., 59, 294–308 (2019) https://doi.org/10.1021/acs.jcim.8b00485
  • I. Hassan, L. Donati, T. Stensitzki, B. G. Keller, K. Heyne,  P. Imhof, “The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations,” Chemical Physics Letters, 698,  227–233 (2018) https://doi.org/10.1016/j.cplett.2018.03.026
  • J. Witek, M. Mühlbauer, B. G. Keller, M. Blatter, A. Meissner, T. Wagner,  S. Riniker, “Interconversion Rates between Conformational States as Rationale for the Membrane Permeability of Cyclosporines.,” ChemPhysChem, 7, 608 (2017) https://doi.org/10.1002/cphc.201700995
  • J. Witek, B. G. Keller, M. Blatter, A. Meissner, T. Wagner,  S. Riniker, “Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States,” J. Chem. Inf. Model., 56, 1547–1562 (2016) https://doi.org/10.1021/acs.jcim.6b00251

  • F. Vitalini, A.S.J.S. Mey, F. Noé, and B.G. Keller “Dynamic Properties of Force Fields” J. Chem. Phys., 142 (2015) p. 084101 https://doi.org/10.1063/1.4909549