Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD and Amide 15 N( 1 H) NMR Relaxation

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Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions

Qiu, Y., Shan, W., & Zhang, H. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00339 · Cited by 23 · see citing works

DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting

Zhang, Z., Cai, Y., Zhang, B., Zheng, W. H., Freddolino, L., Zhang, G., & Zhou, X. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae113 · Cited by 23 · see citing works

NMR spectroscopy on domain dynamics in biomacromolecules

Shapiro, Y. E. (2013) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2013.05.001 · Cited by 20 · see citing works

The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis

Klukowski, P., Damberger, F. F., Allain, F. H. ‐., Iwaï, H., Kadavath, H., Ramelot, T. A., Montelione, G. T., Riek, R., & Güntert, P. (2024) · Scientific Data · doi:10.1038/s41597-023-02879-5 · Cited by 20 · see citing works

TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates

Robson, S. A., Dağ, Ç., Wu, H., & Ziarek, J. J. (2021) · Journal of Biomolecular NMR · doi:10.1007/s10858-021-00379-5 · Cited by 19 · see citing works

Convergent views on disordered protein dynamics from NMR and computational approaches

Salvi, N., Zapletal, V., Jaseňáková, Z., Zachrdla, M., Padrta, P., Narasimhan, S., Marquardsen, T., Tyburn, J., Žı́dek, L., Blackledge, M. J., et al. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.09.016 · Cited by 16 · see citing works

Fitting Force Field Parameters to NMR Relaxation Data

Kümmerer, F., Orioli, S., & Lindorff‐Larsen, K. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00174 · Cited by 16 · see citing works

How to strike a conformational balance in protein force fields for molecular dynamics simulations?

Kang, W., Jiang, F., & Wu, Y. (2021) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1578 · Cited by 16 · see citing works

Using Cross‐Correlated Spin Relaxation to Characterize Backbone Dihedral Angle Distributions of Flexible Protein Segments

Kauffmann, C., Zawadzka‐Kazimierczuk, A., Kontaxis, G., & Konrat, R. (2020) · ChemPhysChem · doi:10.1002/cphc.202000789 · Cited by 15 · see citing works

NMR tools to detect protein allostery

Gampp, O., Kadavath, H., & Riek, R. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102792 · Cited by 13 · see citing works

Super-resolution NMR spectroscopy

Wenchel, L., Gampp, O., & Riek, R. (2024) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2024.107746 · Cited by 13 · see citing works

Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro

Agback, T., Lesovoy, D. M., Han, X. Y., Lomzov, A. A., Sun, R., Sandalova, T., Orekhov, V., Achour, A., & Agback, P. (2023) · Communications Biology · doi:10.1038/s42003-023-05584-6 · Cited by 13 · see citing works

15N transverse relaxation measurements for the characterization of µs–ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange

Kumari, P., Frey, L., Sobol, A., Lakomek, N., & Riek, R. (2018) · Journal of Biomolecular NMR · doi:10.1007/s10858-018-0211-4 · Cited by 12 · see citing works

FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe

Zhao, K., Zhao, P., Wang, S., Xia, Y., & Zhang, G. (2024) · Genome biology · doi:10.1186/s13059-024-03291-x · Cited by 12 · see citing works

The LCP Family Protein, Psr, Is Required for Cell Wall Integrity and Virulence in Streptococcus agalactiae

Rajaei, A., Rowe, H. M., & Neely, M. N. (2022) · Microorganisms · doi:10.3390/microorganisms10020217 · Cited by 11 · see citing works

Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations

Banayan, N. E., Hsu, A., Hunt, J. F., Palmer, A. G. I., & Friesner, R. A. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c00378 · Cited by 9 · see citing works

Cross-relaxation and Cross-correlation Parameters in NMR

(2017) · New developments in NMR · doi:10.1039/9781782622475 · Cited by 8 · see citing works

Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses

Wallerstein, J., Han, X. Y., Levkovets, M., Lesovoy, D. M., Malmodin, D., Mirabello, C., Wallner, B., Sun, R., Sandalova, T., Agback, P., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-06558-y · Cited by 8 · see citing works

Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics

Shen, Y., & Bax, A. (2023) · Structural Dynamics · doi:10.1063/4.0000192 · Cited by 5 · see citing works

Structural insights of an LCP protein–LytR–from Streptococcus dysgalactiae subs. dysgalactiae through biophysical and in silico methods

Paquete-Ferreira, J., Freire, F., Fernandes, H. S., Muthukumaran, J., Ramos, J., Bryton, J., Panjkovich, A., Svergun, D. I., Santos, M. F. A., Correia, M. A. S., et al. (2024) · Frontiers in Chemistry · doi:10.3389/fchem.2024.1379914 · Cited by 5 · see citing works

Hints on experimental techniques

Bertini, I., Luchinat, C., Parigi, G., & Ravera, E. (2016) · Elsevier eBooks · doi:10.1016/b978-0-444-63436-8.00012-0 · Cited by 3 · see citing works

Crystallographic and NMR Study of Streptococcus pneumonia LCP Protein PsrSp Indicate the Importance of Dynamics in Four Long Loops for Ligand Specificity

Sandalova, T., Sala, B. M., Moche, M., Ljunggren, H., Alici, E., Henriques‐Normark, B., Agback, T., Lesovoy, D. M., Agback, P., & Achour, A. (2024) · Crystals · doi:10.3390/cryst14121094 · Cited by 2 · see citing works

PRESERVE: adding variable flip-angle excitation to transverse relaxation-optimized NMR spectroscopy

Brutscher, B. (2024) · Magnetic Resonance · doi:10.5194/mr-5-131-2024 · Cited by 1 · see citing works

Exploring Protein Conformational Ensembles Using Evolutionary Conditional Diffusion

Cui, X., Ge, L., Yang, X., Li, X., Hou, D., Zhou, X., & Zhang, G. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01319 · Cited by 1 · see citing works

Future Prospects for Omics Sciences: Expanding the Boundaries of Systems Biology

Zarid, M. (2026) · Journal of Genome Biotechnology and Genetics · doi:10.3390/jgbg1020008 · Cited by 1 · see citing works

Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein APreprint

Rahimi, K., Halbing, A., Nguyen, M. N., Şen, M., Willson, R. C., & Zerze, G. H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.08.692973

Applications and insights of NMR in enzyme engineering and biocatalysis

Pérez, Y., Moreno, C. J., & Clapés, P. (2026) · Biocatalysis and Biotransformation · doi:10.1080/10242422.2026.2639009

Loop dynamics govern MALT1 activation revealed by integrative AlphaFold, MD, and NMR analysis

Lesovoy, D. M., Agback, T., Roshchin, K., Sandalova, T., Achour, A., Han, X., Lomzov, A. A., Orekhov, V., & Agback, P. (2026) · Scientific Reports · doi:10.1038/s41598-026-53505-4

Exploring Protein Conformational Ensembles Using Evolutionary Conditional Diffusion

Cui, X., Ge, L., Yang, X., Li, X., Hou, D., Zhou, X., & Zhang, G. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01319 · Cited by 1 · see citing works

Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement

Gong, Z., Gu, X., Guo, D., Wang, J., & Tang, C. (2016) · Angewandte Chemie · doi:10.1002/ange.201609830 · Cited by 4 · see citing works

Determining protein conformational ensembles by combining machine learning and small-angle scattering

Lidbrink, S. E., Haloi, N., Howard, R. J., & Lindahl, E. R. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2023.11.2610 · Cited by 1 · see citing works

EnsembleFlex: Protein structure ensemble analysis made easy

Schneider, M., Márquez, J. A., & Leach, A. R. (2025) · Structure · doi:10.1016/j.str.2025.07.001 · Cited by 4 · see citing works

Predicting protein dynamics from structural ensembles

Copperman, J., & Guenza, M. G. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4935575 · Cited by 16 · see citing works