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Density-based cluster algorithms allow for an efficient and reliable identification of core-sets

identification of core sets.

Allosteric network the C-type lectin receptor Langerin

modulates the Ca2+-affinity of this receptor.

Cyclosporin exhibits congruent states

in polar and apolar solvents.

Comparison of variational approach and conventional Markov model

for the hexapeptide VGVAPG. With the new basis set for peptides for the variational approach one can directly interpret the eigenvectors are conformational changes.

Illustration of the concept of dimer interface characterization

to elucidate the inhibition paradigm of HIV-1 protease by application of
the computational alanine scanning mutagenesis (ASM) method to molecular dynamics (MD) simulations.

Slow conformational dynamics of alanine dipeptide and deca-alanine

when simulated with two different force fields. Different force fields yield different conformational dynamics (J. Chem. Phys. 142(2015), 084101).

Complex RNA folding kinetic

revealed by single-molecule FRET and hidden Markov models

(J. Am. Chem. Soc. (appeared online, DOI 10.1021/ja4098719))

Helix-coil transition

Helix-coil transition of deca-alanine as identified by a variational approach to molecular kinetics.

J. Chem. Theory Comput. (appeared online, DOI: 10.1021/ct4009156)

Metastable states

Metastable states of a beta-peptide identified by a kinetic cluster algorithm.

(J. Chem. Phys. 132, 074110 (2010))

Transition Matrices in the non-Markovian regime

Validity of Markov state models for emulating the dynamics of classical molecular systems and ensembles

(J. Chem. Theory Comp., 7 (2011), p. 1032-1044)

Molecular Dynamics

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