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metadynminer
D. Trapl & V. Spiwok: Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d R Journal 2022, 14(3) 46-58.
alphafold
V. Spiwok, M. Kurečka & A. Křenek: Collective Variable for Metadynamics Derived from AlphaFold Output Front. Mol. Biosci. 2022, 9 878133.
pmff
D. Trapl, M. Krupička, V. Višňovský, J. Hozzová, J. Oľha, A. Křenek & V. Spiwok: Property map collective variable as a useful tool for force field correction J. Chem. Inf. Model. 2022, 62(3) 567-576.
fmb
P. Kříž & V. Spiwok: Time-Lagged t-Distributed Stochastic Neighbor Embedding (t-SNE) of Molecular Simulation Trajectories. Front. Mol. Biosci. 2020, 7, 132.
fmb
D. Trapl, I. Horvacanin, V. Mareska, F. Ozcelik, G. Unal & V. Spiwok: Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations. Front. Mol. Biosci. 2019, 6, 25.
jpcb
P. Kříž, Z. Šućur & V. Spiwok: Free Energy Surface Prediction by Flying Gaussian Method: Multi-System Representation. J. Chem. Phys. 2017, 121(46) 10479-10483.
jpcb
P. Hošek, P. Kříž, D. Toulcová, & V. Spiwok: Multisystem Altruistic Metadynamics – Well-Tempered Variant. J. Chem. Phys. 2017, 146, 125103.
jpcb
J. Pazúriková, A. Křenek, V. Spiwok & M. Šimková: Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics. J. Chem. Phys. 2017, 146, 115101.
jpcb
Z. Šućur & V. Spiwok: Sampling Enhancement and Free Energy Prediction by Flying Gaussian Method. J. Chem. Theory Comput. 2016, 12(9), 4644-4650.
jpcb
P. Hošek, D. Toulcová, A. Bortolato & V. Spiwok: Altruistic Metadynamics: Multisystem Biased Simulation. J. Phys. Chem. B 2016, 120(9), 2209-2215.
cpc
P. Hošek & V. Spiwok: Metadyn View: Fast Web-Based Viewer of Free Energy Surfaces Calculated by Metadynamics. Comput. Phys. Commun. 2016, 198, 222-229.
jcp
V. Spiwok, P. Oborský, J. Pazúriková, A. Křenek & B. Králová: Nonlinear vs. Linear Biasing in Trp-cage Folding Simulations. J. Chem. Phys. 2015, 142, 115101.