Current opinion in structural biology

DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

(2024) · doi:10.1038/s41467-024-45461-2 · Cited by 243

3D molecular generative framework for interaction-guided drug design

(2024) · doi:10.1038/s41467-024-47011-2 · Cited by 88

Redox Regulation of Ap-1

Xanthoudakis, S., & Curran, T. (1996) · Advances in Experimental Medicine and Biology · doi:10.1007/978-1-4757-9480-9_10 · Cited by 63

Evolutionary innovations and the organization of protein functions in genotype space

Ferrada, E., & Wagner, A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014172 · Cited by 51

Explore Protein Conformational Space With Variational Autoencoder

Tian, H., Jiang, X., Trozzi, F., Xiao, S., Larson, E. C., & Tao, P. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.781635 · Cited by 51

A Structure-Based View on ABC-Transporter Linked to Multidrug Resistance

(2023) · doi:10.3390/molecules28020495 · Cited by 48

EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

Shao, Q., Jiang, Y., & Yang, Z. J. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01424 · Cited by 43

Representing structures of the multiple conformational states of proteins

Ramelot, T. A., Tejero, R., & Montelione, G. T. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102703 · Cited by 26

Basis for Accurate Protein p K a Prediction with Machine Learning

Cai, Z., Liu, T., Lin, Q., He, J., Lei, X., Luo, F., & Huang, Y. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00254 · Cited by 31

Mutexa: A Computational Ecosystem for Intelligent Protein Engineering

Yang, Z. J., Shao, Q., Jiang, Y., Jurich, C., Ran, X., Juarez, R. J., Yan, B., Stull, S. L., Gollu, A., & Ding, N. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00602 · Cited by 28

Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

Jankowski, M. S., Griffith, D., Shastry, D. G., Pelham, J. F., Ginell, G. M., Thomas, J., Karande, P., Holehouse, A. S., & Hurley, J. M. (2024) · Nature Communications · doi:10.1038/s41467-024-47761-z · Cited by 23

Arabidopsis calmodulin‐like proteins CML13 and CML14 interact with proteins that have IQ domains

Teresinski, H. J., Hau, B., Symonds, K., Kilburn, R., Munro, K. A., Doner, N. M., Mullen, R., Li, V. H., & Snedden, W. A. (2023) · Plant, Cell & Environment · doi:10.1111/pce.14616 · Cited by 21

Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures

Villard, J., Kılıç, M., & Rothlisberger, U. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c01078 · Cited by 19

How Robust Is the Ligand Binding Transition State?

Bose, S., Lotz, S. D., Deb, I., Shuck, M., Lee, K. S. S., & Dickson, A. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c08940 · Cited by 16

Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2

(2025) · doi:10.1038/s41467-025-55942-7 · Cited by 15

The immune interactions of gut glycans and microbiota in health and disease

(2024) · doi:10.1111/mmi.15267 · Cited by 14

Structural motif search across the protein universe with Folddisco

Kim, H., Kim, R. S., Mirdita, M., Yoon, J., & Steinegger, M. (2026) · Nature Biotechnology · doi:10.1038/s41587-026-03162-9 · Cited by 10

“Dividing and Conquering” and “Caching” in Molecular Modeling

Cao, X., & Tian, P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22095053 · Cited by 10

An artificial neural network model to predict structure-based protein–protein free energy of binding from Rosetta-calculated properties

Ferraz, M. V. F., Neto, J. C. S., Lins, R. D., & Teixeira, E. S. (2023) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp05644e · Cited by 9

Prediction of order parameters based on protein NMR structure ensemble and machine learning

Wang, Q., Miao, Z., Xiao, X., Zhang, X., Yang, D., Jiang, B., & Liu, M. (2024) · Journal of Biomolecular NMR · doi:10.1007/s10858-024-00435-w · Cited by 9

Conformational landscapes of rigid and flexible molecules explored with variable temperature ion mobility-mass spectrometry

Wang, X., Norgate, E., Dai, J., Benoit, F., Bristow, T., England, R. M., Kalapothakis, J. M. D., & Barran, P. E. (2025) · Nature Communications · doi:10.1038/s41467-025-59065-x · Cited by 7

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

Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Orekhov, V., & Agback, P. (2025) · doi:10.1101/2025.02.07.637034 · Cited by 6

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

Lesovoy, D., Roshchin, K., Sala, B. M., Sandalova, T., Achour, A., Agback, T., Agback, P., & Orekhov, V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26188917 · Cited by 6

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

Michaelis, M., Cupellini, L., Mensch, C., Perry, C. C., Delle Piane, M., & Colombi Ciacchi, L. (2023) · Chemical Science · doi:10.1039/d3sc02202a · Cited by 6

TMVisDB: Annotation and 3D-visualization of Transmembrane Proteins

Olenyi, T., Marquet, C., Grekova, A., Houri, L., Heinzinger, M., Dallago, C., & Rost, B. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.168997 · Cited by 4

Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner

Choi, J. (2023) · iScience · doi:10.1016/j.isci.2023.106911 · Cited by 1