The role of dynamic conformational ensembles in biomolecular recognition

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Impact of protein conformational diversity on AlphaFold predictions

Saldaño, T., Escobedo, N., Marchetti, J., Zea, D. J., Mac Donagh, J., Velez Rueda, A. J., Gonik, E., García Melani, A., Novomisky Nechcoff, J., Salas, M. N., et al. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac202 · Cited by 196 · see citing works

AlphaFold, Artificial Intelligence (AI), and Allostery

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works

Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics

Iversen, L., Tu, H.-L., Lin, W.-C., Christensen, S. M., Abel, S. M., Iwig, J., Wu, H.-J., Gureasko, J., Rhodes, C., Petit, R. S., et al. (2014) · Science · doi:10.1126/science.1250373 · Cited by 154 · see citing works

Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Serganov, A., & Patel, D. J. (2012) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-101211-113224 · Cited by 160 · see citing works

Principles of Allosteric Interactions in Cell Signaling

Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154 · see citing works

Exploring the role of receptor flexibility in structure-based drug discovery

Feixas, F., Lindert, S., Sinko, W., & McCammon, J. A. (2014) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.007 · Cited by 156 · see citing works

The Design of Covalent Allosteric Drugs

Nussinov, R., & Tsai, C.-J. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124401 · Cited by 112 · see citing works

Protein Conformational Populations and Functionally Relevant Substates

Ramanathan, A., Savol, A., Burger, V., Chennubhotla, C. S., & Agarwal, P. K. (2014) · Accounts of Chemical Research · doi:10.1021/ar400084s · Cited by 110 · see citing works

Cooperative Unfolding of Compact Conformations of the Intrinsically Disordered Protein Osteopontin

Kurzbach, D., Platzer, G., Schwarz, T. C., Henen, M. A., Konrat, R., & Hinderberger, D. (2013) · Biochemistry · doi:10.1021/bi400502c · Cited by 105 · see citing works

Structure-based prediction of protein allostery

Greener, J. G., & Sternberg, M. J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.002 · Cited by 91 · see citing works

Information transfer by leaky, heterogeneous, protein kinase signaling systems

Voliotis, M., Perrett, R. M., McWilliams, C., McArdle, C. A., & Bowsher, C. G. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314446111 · Cited by 98 · see citing works

RNA-guided assembly of Rev-RRE nuclear export complexes

Bai, Y., Tambe, A., Zhou, K., & Doudna, J. A. (2014) · eLife · doi:10.7554/elife.03656 · Cited by 86 · see citing works

Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit

Greives, N., & Zhou, H.-X. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1407545111 · Cited by 82 · see citing works

Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase

Jensen, S. B., Thodberg, S., Parween, S., Moses, M. E., Hansen, C. C., Thomsen, J., Sletfjerding, M. B., Knudsen, C., Del Giudice, R., Lund, P. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22562-w · Cited by 64 · see citing works

Protein flexibility in drug discovery: from theory to computation.

Buonfiglio, R., Recanatini, M., & Masetti, M. (2015) · ChemMedChem · doi:10.1002/cmdc.201500086 · Cited by 73 · see citing works

Mechanisms of ligand binding

Di Cera, E. (2020) · Biophysics Reviews · doi:10.1063/5.0020997 · Cited by 73 · see citing works

“Pathway drug cocktail”: targeting Ras signaling based on structural pathways

Nussinov, R., Tsai, C.-J., & Mattos, C. (2013) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2013.07.009 · Cited by 62 · see citing works

Critical Scaffolding Regions of the Tumor Suppressor Axin1 Are Natively Unfolded

Noutsou, M., Duarte, A. M. S., Anvarian, Z., Didenko, T., Minde, D. P., Kuper, I., de Ridder, I., Oikonomou, C., Friedler, A., Boelens, R., et al. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.11.013 · Cited by 58 · see citing works

Allosteric Conformational Barcodes Direct Signaling in the Cell

Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure · doi:10.1016/j.str.2013.06.002 · Cited by 55 · see citing works

Conformational Recognition of an Intrinsically Disordered Protein

Krieger, J. M., Fusco, G., Lewitzky, M., Simister, P. C., Marchant, J., Camilloni, C., Feller, S. M., & De Simone, A. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.03.004 · Cited by 56 · see citing works

An ensemble of flexible conformations underlies mechanotransduction by the cadherin–catenin adhesion complex

Bush, M., Alhanshali, B. M., Qian, S., Stanley, C. B., Heller, W. T., Matsui, T., Weiss, T. M., Nicholl, I. D., Walz, T., Callaway, D. J. E., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1911489116 · Cited by 42 · see citing works

Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems

Kurkcuoglu, Z., & Bonvin, A. M. J. J. (2020) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25802 · Cited by 37 · see citing works

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations

Xia, J., Deng, N.-J., & Levy, R. M. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp400797y · Cited by 29 · see citing works

Protein multiple conformations prediction using multi-objective evolution algorithm

Hou, M.-H., Jin, S.-R., Cui, X.-Y., Peng, C.-X., Zhao, K.-L., Song, L., & Zhang, G.-J. (2023) · doi:10.1101/2023.04.21.537776 · Cited by 29 · see citing works

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Bohnuud, T., Kozakov, D., & Vajda, S. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003872 · Cited by 27 · see citing works

Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations

Qin, H., Lim, L., & Song, J. (2012) · BMC Biophysics · doi:10.1186/2046-1682-5-2 · Cited by 23 · see citing works

Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints

Zhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2025) · Communications Biology · doi:10.1038/s42003-025-08783-5 · Cited by 19 · see citing works

Quantitatively accounting for protein reorganization in computer-aided drug design

Fajer, M., Borrelli, K., Abel, R., & Wang, L. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00009 · Cited by 18 · see citing works

Dynamic Protein Allosteric Regulation and Disease

Nussinov, R., Tsai, C.-J., & Jang, H. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-981-13-8719-7_2 · Cited by 18 · see citing works

Impact of protein conformational diversity on AlphaFold predictions

Saldaño, T., Escobedo, N., Marchetti, J., Zea, D. J., Mac Donagh, J., Velez Rueda, A. J., Gonik, E., Melani, A. G., Novomisky Nechcoff, J., Salas, M. N., et al. (2021) · doi:10.1101/2021.10.27.466189 · Cited by 196 · see citing works

Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations

Huan, X., Shi, J., Lim, L., Mitra, S., Zhu, W., Qin, H., Pasquale, E. B., & Song, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074040 · Cited by 16 · see citing works

Ensemble-based characterization of unbound and bound states on protein energy landscape

Ruvinsky, A. M., Kirys, T., Tuzikov, A. V., & Vakser, I. A. (2013) · Protein Science · doi:10.1002/pro.2256 · Cited by 9 · see citing works

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 · see citing works

CCProf: exploring conformational change profile of proteins

Chang, C.-W., Chou, C.-W., & Chang, D. T.-H. (2016) · Database · doi:10.1093/database/baw029 · Cited by 10 · see citing works

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking

Dobbins, S. E., Lesk, V. I., & Sternberg, M. J. E. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802496105 · Cited by 226 · see citing works

Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

Wako, H., & Endo, S. (2011) · Biophysical Chemistry · doi:10.1016/j.bpc.2011.07.004 · Cited by 32 · see citing works

148 Evolutionary dynamics of conformational flexibility

Ortiz, J. F., Masterson, P., MacDonald, M. L., et al. (2013) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2013.786390

Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions

Shao, Q. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp05634b · Cited by 20 · see citing works