Biomolecular Dynamics @ Uni Freiburg


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Journal of Chem. Physics



Perspective: Identification of collective variables and metastable states of protein dynamics,
F. Sittel and G. Stock
J. Chem. Phys 149, 150901(2018) pdf*  147
MELD-path efficiently computes conformational transitions, including multiple and diverse paths,
A. Perez, F. Sittel, G. Stock, and K. Dill
J. Chem. Theory Comput 14, 2109 (2018) pdf** 146
Machine Learning of Biomolecular Reaction Coordinates,
S.Brandt, F. Sittel, M. Ernst, and G. Stock
J. Phys. Chem. Lett. 9, 2144 (2018) pdf** si 145
A Nonequilibrium Approach to Allosteric Communication,
G. Stock, and P. Hamm
Phil. Trans. B 373, 20170187 (2018) pdf*  144
Metadynamics Enhanced Markov Modeling of Protein Dynamics,
M. Biswas, B. Lickert, and G. Stock
J. Phys. Chem. B 122, 5508 (2018) pdf** si 143


Principal component analysis on a torus: Theory and application to protein dynamics,
F. Sittel, T. Filk, and G. Stock
J. Chem. Phys 147, 244101 (2017) pdf* si 142
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2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain,
B. Stucki-Buchli, P. J. M. Johnson, O. Bozovic, C. Zanobini, K. L. Koziol, P. Hamm, A. Gulzar, S. Wolf, S. Buchenberg, and G. Stock
J. Phys. Chem. A 121, 9435 (2017) pdf** si 141
Identification and Validation of Reaction Coordinates Describing Protein Functional Motion: Hierarchical Dynamics of T4 Lysozyme,
M. Ernst, S. Wolf, and G. Stock
J. Chem. Theory Comput 13, 5076 (2017) pdf** si  140
Time-resolved observation of protein allosteric communication,
S. Buchenberg, F. Sittel, and G. Stock
PNAS 114, 33, E6804 (2017) pdf si 139
Vibrational energy transport in acetyl benzonitrile described by an ab initio-based quantum tier model,
H. Fujisaki, K. Yagi, H. Kikuchi, T. Takami, and G. Stock
Chem. Phys. 482, 86 (2017) pdf 138


Global Langevin model of multidimensional biomolecular dynamics,
N. Schaudinnus, B. Lickert, M. Biswas, and G. Stock
J. Chem. Phys. 145, 184114 (2016) pdf* si 137
Mechanisms for allosteric activation of protease DegS by ligand binding and oligomerization as revealed from molecular dynamics simulations,
C. Lu, G. Stock, and V. Knecht
Proteins: Structure, Function and Bioinformatics 84, 1690 (2016) pdf si 136
Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins,
F. Sittel, and G. Stock
J. Chem. Theory Comput 12, 2426 (2016) pdf** si  135
Long-Range Conformational Response of a PDZ Domain to Ligand Binding and Release: A Molecular Dynamics Study,
C. Lu, V. Knecht, and G. Stock
J. Chem. Theory Comput 12, 870 (2016) pdf** si  134
Scaling Rules for Vibrational Energy Transport in Globular Proteins,
S. Buchenberg, D. M. Leitner, and G. Stock
J. Phys. Chem. Lett. 7, 25 (2016) pdf** si  133


Contact- and distance-based principal component analysis of protein dynamics,
M. Ernst, F. Sittel, and G. Stock
J. Chem. Phys. 143, 244114 (2015) pdf* si  132
Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes,
P. D. Dixit, A. Jain, G. Stock, and K. A. Dill
J. Chem. Theory Comput. 11, 5464 (2015) pdf**  131
Nonadiabatic vibrational dynamics in the HCO 2 H 2 O complex,
P. Hamm,and G. Stock
J. Chem. Phys. 143, 134308 (2015) pdf*  130
Multidimensional Langevin modeling of nonoverdamped dynamics,
N. Schaudinnus, B. Bastian, R. Hegger,and G. Stock
Phys. Rev. Lett. 115, 050602 (2015) pdf***  129
Hierarchical biomolecular dynamics: Picosecond hydrogen bonding regulates micro-second conformational transitions,
S. Buchenberg, N. Schaudinnus, and G. Stock
J. Chem. Theory Comput. 11, 1330 (2015) pdf** si  128
Vibrational energy flow in the villin headpiece subdomain: Master equation simulations,
D. Leitner, S. Buchenberg, P. Brettl, and G. Stock
J. Chem. Phys. 141, 075101 (2015) pdf*  127


Communication: Microsecond peptide dynamics from nanosecond trajectories: A Langevin approach,
R. Rzepiela, N. Schaudinnus, S. Buchenberg, R. Hegger, and G. Stock
J. Chem. Phys. 141, 241102 (2014) pdfsi 126
Long-Range Conformational Transition of a Photoswitchable Allosteric Protein: Molecular Dynamics Simulation Study,
S. Buchenberg, V. Knecht, R. Walser, P. Hamm and G. Stock
J. Phys. Chem. B 118, 13468 (2014) pdf** si  125
Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates,
F. Sittel, A. Jain and G. Stock
J. Chem. Phys. 141, 014111 (2014) pdf* si  124
Hierarchical folding free energy landscape of HP35 revealed by most probable path clustering,
A. Jain and G. Stock
J. Phys. Chem. B 118, 7750 (2014) pdf** si  123


Wolfgang Domcke zum 65. Geburtstag,
G. Stock and M. Thoss
Bunsenmagazin 2, 56 (2013) pdf  122
Data driven Langevin modeling of biomolecular dynamics,
N. Schaudinnus, A. J. Rzepiela, R. Hegger, and G. Stock
J. Chem. Phys. 138, 204106 (2013) pdf*   121
Vibrational conical intersections in the water dimer,
P. Hamm and G. Stock
Molecular Physics 111, 2046 (2013) pdf****  120


Effect of the ion treatment on an RNA hairpin: molecular dynamics study,
E. C. Widjajakusuma, A. Villa, and G. Stock
Indo. J. Chem. 12, 1 (2012) pdf   119
Vibrational conical intersections as mechanism of ultrafast vibrational relaxation,
P. Hamm, and G. Stock
Phys. Rev. Lett. 109, 173201 (2012) pdf***   118
Identifying metastable states of folding proteins,
A. Jain, and G. Stock,
J. Comp. Theo. Chem. 8, 3810 (2012) pdf**   117
Construction of the free energy landscape of peptide aggregation from molecular dynamics simulations,
L. Riccardi, P. H Phuong, and G. Stock,
J. Comp. Theo. Chem. 8, 1471 (2012) pdf**   116
Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations,
G. Stock, A. Jain, L. Riccardi, and P. H. Nguyen
in: Protein and Peptide Folding, Misfolding and Non-Folding, ed. R. Schweitzer-Stenner, Wiley, New York, 57 (2012) pdf   115


Simulation of transient infrared spectra of a photoswitchable peptide,
M. Kobus, M. Lieder, P. H. Nguyen, and G. Stock,
J. Chem. Phys. 135, 225102 (2011) pdf*  114
Real time observation of ultrafast peptide conformational dynamics: Molecular Dynamics simulation vs. Infrared experiment,
P. H. Nguyen, H. Staudt, J. Wachtveitl, and G. Stock,
J. Phys. Chem. B 115, 13084 (2011) pdf**  113
Coherent vibrational energy transfer along a peptide helix,
M. Kobus, P. H. Nguyen, and G. Stock,
J. Chem. Phys. 134, 124518 (2011) pdf*  112


Hidden complexity of protein free-energy landscapes revealed by principal component analysis by parts,
A. Jain, R. Hegger, and G. Stock,
J. Phys. Chem. Lett. 1, 2769 (2010) pdf  111
Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study,
M. Kobus, P. H. Nguyen, and G. Stock,
J. Chem. Phys. 133, 034512 (2010) pdf*  110
Maximum caliber inference of nonequilibrium processes,
M. Otten and G. Stock,
J. Chem. Phys.133, 034119 (2010) pdf*  109
Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix,
P. H. Nguyen, S. M. Park, and G. Stock,
J. Chem. Phys.132, 025102 (2010) pdf*  108

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