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Conformational Flexibility of Human Casein Kinase Catalytic Subunit Explored by Metadynamics

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Exploring chemical reactivity of complex systems with path‐based coordinates: Role of the distance metric

Zinovjev, K., & Tuñón, I. (2014) · Journal of Computational Chemistry · doi:10.1002/jcc.23673 · Cited by 19 · see citing works

All-Atom Molecular Dynamics Simulations of β-Hairpins Stabilized by a Tight Turn: Pronounced Heterogeneous Folding Pathways

Kim, J., & Keiderling, T. A. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp912159t · Cited by 17 · see citing works

Photocontrolled chignolin-derived β-hairpin peptidomimetics

Podewin, T., Rampp, M. S., Turkanovic, I., Karaghiosoff, K., Zinth, W., & Hoffmann‐Röder, A. (2015) · Chemical Communications · doi:10.1039/c4cc10304a · Cited by 17 · see citing works

The opposing effect of urea and high pressure on the conformation of the protein β-hairpin: A molecular dynamics simulation study

Borgohain, G., & Paul, S. (2017) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2017.12.054 · Cited by 16 · see citing works

The effects of side chain hydrophobicity on the denaturation of simple β-hairpins

Wei, H., Shao, Q., & Gao, Y. Q. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/b924593f · Cited by 16 · see citing works

Simulations of flow induced structural transition of the β-switch region of glycoprotein Ibα

Han, M., Xu, J., Ren, Y., & Li, J. (2015) · Biophysical Chemistry · doi:10.1016/j.bpc.2015.11.002 · Cited by 16 · see citing works

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

Pucheta-Martínez, E., D’Amelio, N., Lelli, M., Martinez-Torrecuadrada, J. L., Sudol, M., Saladino, G., & Gervasio, F. L. (2016) · Scientific Reports · doi:10.1038/srep30293 · Cited by 16 · see citing works

Free energy along drug-protein binding pathways interactively sampled in virtual reality

Deeks, H. M., Zinovjev, K., Barnoud, J., Mulholland, A. J., van der Kamp, M. W., & Glowacki, D. R. (2023) · Scientific Reports · doi:10.1038/s41598-023-43523-x · Cited by 15 · see citing works

Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece

Saladino, G., Marenchino, M., & Gervasio, F. L. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct2002489 · Cited by 15 · see citing works

Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch

Zou, X., Liu, Y., Chen, Z., Cárdenas‐Jirón, G., & Schulten, K. J. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2010.05.035 · Cited by 15 · see citing works

β-hairpin forms by rolling up from C-terminal: Topological guidance of early folding dynamics

Enemark, S., Kurniawan, N. A., & Rajagopalan, R. (2012) · Scientific Reports · doi:10.1038/srep00649 · Cited by 14 · see citing works

Exact partition function zeros of the Wako-Saitô-Muñoz-Eaton β hairpin model

Lee, J. (2013) · Physical Review E · doi:10.1103/physreve.88.022710 · Cited by 13 · see citing works

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

Peter, E. K., Shea, J., & Pivkin, I. V. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp06867c · Cited by 12 · see citing works

Long-range dynamic correlations regulate the catalytic activity of the bacterial tyrosine kinase Wzc

Hajredini, F., Piserchio, A., & Ghose, R. (2020) · Science Advances · doi:10.1126/sciadv.abd3718 · Cited by 11 · see citing works

Infrared Study of the Stability and Folding Kinetics of a Series of β-Hairpin Peptides with a Common NPDG Turn

Xu, Y., Du, D., & Oyola, R. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp2046867 · Cited by 11 · see citing works

Transition state ensemble optimization for reactions of arbitrary complexity

Zinovjev, K., & Tuñón, I. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4931596 · Cited by 10 · see citing works

Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules

Maccari, G., Mori, M., Rodríguez‐Salarichs, J., Fang, W., Díaz, J. F., & Botta, M. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct3006612 · Cited by 10 · see citing works

Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

Michaelis, M., Hildebrand, N., Meißner, R. H., Wurzler, N., Li, Z., Hirst, J. D., Micsonai, A., Kardos, J., Piane, M. D., & Ciacchi, L. C. (2019) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.9b03932 · Cited by 10 · see citing works

The universality of β-hairpin misfolding indicated by molecular dynamics simulations

Shao, Q., Wang, J., Shi, J., & Zhu, W. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4826461 · Cited by 10 · see citing works

Dynamics of Structural Elements of GB1 β-Hairpin Revealed by Tryptophan–Cysteine Contact Formation Experiments

Soranno, A., Cabassi, F., Orselli, M. E., Cellmer, T., Gori, A., Longhi, R., & Buscaglia, M. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b07399 · Cited by 9 · see citing works

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers

Meloni, R., Camilloni, C., & Tiana, G. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400879v · Cited by 8 · see citing works

Effective Conformational Sampling in Explicit Solvent with Gaussian Biased Accelerated Molecular Dynamics

Shao, Q., & Zhu, W. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00242 · Cited by 8 · see citing works

Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin.

Jimenez-Cruz, C., & Garcia, A. (2014) · Physical Chemistry, Chemical Physics - PCCP · doi:10.1039/c3cp54336f · Cited by 6 · see citing works

Can molecular dynamics be used to simulate biomolecular recognition?

Lüking, M., van der Spoel, D., Elf, J., & Tribello, G. A. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0146899 · Cited by 6 · see citing works

Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

Rigoli, M., Spagnolli, G., Lorengo, G., Monti, P., Potestio, R., Biasini, E., & Inga, A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23147960 · Cited by 6 · see citing works

Cyclic β-Helical/β-Hairpin d , l -α-Peptide: Study of Its Folding Properties and Structure Refinement Using Molecular Dynamics

Meier, K., & A, W. F. V. G. (2010) · The Journal of Physical Chemistry A · doi:10.1021/jp906218f · Cited by 6 · see citing works

The sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core

Gupta, M., Khatua, P., Chakravarty, C., & Bandyopadhyay, S. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp03825a · Cited by 6 · see citing works

Ligand-Binding Calculations with Metadynamics.

Provasi, D. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9608-7_10 · Cited by 5 · see citing works

Investigating structural biophysical features for antigen-binding fragment crystallization via machine learning

Chattaraj, K. G., Ferreira, J., Myerson, A. S., & Trout, B. L. (2025) · Molecular Systems Design & Engineering · doi:10.1039/d4me00187g · Cited by 5 · see citing works

The nature of persistent interactions in two model β‐grasp proteins reveals the advantage of symmetry in stability

Bedford, J. T., Poutsma, J. L., Diawara, N., & Greene, L. H. (2021) · Journal of Computational Chemistry · doi:10.1002/jcc.26477 · Cited by 4 · see citing works

Diffusion over barriers

Peters, B. (2017) · Elsevier eBooks · doi:10.1016/b978-0-44-456349-1.00018-0 · Cited by 3 · see citing works

Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β -hairpin peptide

Daidone, I., Polzi, L. Z., Thukral, L., Alekozai, E. M., & Amadei, A. (2016) · Chemical Physics Letters · doi:10.1016/j.cplett.2016.07.041 · Cited by 3 · see citing works

Advances in Molecular Simulation

Aldeghi, M., & Biggin, P. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12343-1 · Cited by 2 · see citing works

Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations

Meloni, R., & Tiana, G. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25255 · Cited by 3 · see citing works

Polyelectrolyte Influence on Beta-Hairpin Peptide Stability: A Simulation Study

Moses, K., & Tassel, P. R. V. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c06641 · Cited by 2 · see citing works

Exploring the free energy landscape of a model β-hairpin peptide and its isoform

Narayanan, C., & Dias, C. L. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24601 · Cited by 2 · see citing works

Diverse Protein-Folding Pathways and Functions of β-Hairpins and β-Sheets

Balusek, C., Hwang, H. J., Hazel, A. J., Lundquist, K. P., Pavlova, À., & Gumbart, J. C. (2018) · Springer eBooks · doi:10.1007/978-3-319-73975-5_1 · Cited by 1 · see citing works

Using Molecular Simulations and Metadynamics to Predict Binding Free Energies and Kinetics: the Case of Cox and Cdk2

Saladino, G., & Gervasio, F. L. (2012) · Royal Society of Chemistry eBooks · doi:10.1039/9781849735377-00360

The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes

Zinovjev, K., Ruiz‐Pernía, J. J., & Tuñón, I. (2025) · Pure and Applied Chemistry · doi:10.1515/pac-2025-0500 · Cited by 1 · see citing works

Les avancées de la modélisation en biochimie : des méthodes mixtes QM/MM à la métadynamique

Gouron, A. (2014) · doi:10.70675/41da6cfdz8387z43bcz8fe7z0e027d6d98fc

Metadynamics Simulations of Nucleation

Ronneberger, I., & Mazzarello, R. (2015) · Springer series in materials science · doi:10.1007/978-3-319-15675-0_3

Non-Native Structure in the Unfolded Ensemble of a Prototypical β-Hairpin

Bonomi, M., Branduardi, D., Gervasio, F. L., & Parrinello, M. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.12.307

Free energy landscape and folding mechanism of a β‐hairpin in explicit water: A replica exchange molecular dynamics study

Nguyen, P. H., Stock, G., Mittag, E., Hu, C., & Li, M. S. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20696 · Cited by 129 · see citing works

Understanding β-Hairpin Formation by Molecular Dynamics Simulations of Unfolding

Lee, J., & Shin, S. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)75896-1 · Cited by 43 · see citing works

Understanding how Beta-Hairpins Fold using Molecular Dynamics Simulations in Multiple Force Fields

Husic, B. E., McKiernan, K. A., & Pande, V. S. (2018) · Biophysical Journal · doi:10.1016/j.bpj.2017.11.1167

Common Folding Mechanism of a β-Hairpin Peptide via Non-native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations

Thukral, L., Smith, J. C., & Daidone, I. (2009) · Journal of the American Chemical Society · doi:10.1021/ja9064365 · Cited by 36 · see citing works