Protein dynamics and conformational selection in bidirectional signal transduction

Molecular dynamics simulations and drug discovery

Durrant, J. D., & McCammon, J. A. (2011) · BMC Biology · doi:10.1186/1741-7007-9-71 · Cited by 1,412 · see citing works

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

Lange, O. F., Lakomek, N., Farès, C., Schroeder, G. F., Walter, K. F. A., Becker, S., Meiler, J., Grubmüller, H., Griesinger, C., & de Groot, B. L. (2008) · Science · doi:10.1126/science.1157092 · Cited by 1,044 · see citing works

Protein kinases: evolution of dynamic regulatory proteins

Taylor, S. S., & Kornev, A. P. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.09.006 · Cited by 940 · see citing works

Folding funnels and binding mechanisms

Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594 · see citing works

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

del Sol, A., Tsai, C., Ma, B., & Nussinov, R. (2009) · Structure · doi:10.1016/j.str.2009.06.008 · Cited by 365 · see citing works

Crystal structure of an Eph receptor–ephrin complex

Himanen, J., Rajashankar, K. R., Lackmann, M., Cowan, C. A., Henkemeyer, M. J., & Nikolov, D. B. (2001) · Nature · doi:10.1038/414933a · Cited by 339 · see citing works

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

Włodarski, T., & Žagrović, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906966106 · Cited by 194 · see citing works

Eph, a Protein Family Coming of Age: More Confusion, Insight, or Complexity?

Lackmann, M., & Boyd, A. (2008) · Science Signaling · doi:10.1126/stke.115re2 · Cited by 150 · see citing works

Structural Plasticity of Eph Receptor A4 Facilitates Cross-Class Ephrin Signaling

Bowden, T. A., Aricescu, A. R., Nettleship, J. E., Siebold, C., Rahman-Huq, N., Owens, R. J., Stuart, D. I., & Jones, E. Y. (2009) · Structure · doi:10.1016/j.str.2009.07.018 · Cited by 95 · see citing works

In Silico Elucidation of the Recognition Dynamics of Ubiquitin

Long, D., & Brüschweiler, R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002035 · Cited by 47 · see citing works

Amplification of signaling via cellular allosteric relay and protein disorder

Ma, B., & Nussinov, R. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903024106 · Cited by 36 · see citing works

How do dynamic cellular signals travel long distances?

Nussinov, R. (2011) · Molecular BioSystems · doi:10.1039/c1mb05205e · Cited by 33 · 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

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

Ras Conformational Ensembles, Allostery, and Signaling

Lu, S., Jang, H., Muratcioglu, S., Gursoy, A., Keskin, O., Nussinov, R., & Zhang, J. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00542 · Cited by 355 · see citing works

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

Chowdhury, D. (2013) · Physics Reports · doi:10.1016/j.physrep.2013.03.005 · Cited by 218 · see citing works

DeepDTAF: a deep learning method to predict protein–ligand binding affinity

Wang, K., Zhou, R., Li, Y., & Li, M. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab072 · Cited by 213 · see citing works

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 174 · 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

Flexible receptor docking for drug discovery

Wong, C. F. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1078308 · Cited by 75 · see citing works

An overview of recent advances in structural bioinformatics of protein–protein interactions and a guide to their principles

Sudha, G., Nussinov, R., & Srinivasan, N. (2014) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2014.07.004 · Cited by 69 · see citing works

CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

Monzón, A. M., Rohr, C., Fornasari, M. S., & Parisi, G. D. (2016) · Database · doi:10.1093/database/baw038 · Cited by 68 · see citing works

The principle of conformational signaling

Tompa, P. (2016) · Chemical Society Reviews · doi:10.1039/c6cs00011h · Cited by 63 · see citing works

NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding

Cembran, A., Kim, J., Gao, J., & Veglia, G. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp00110a · Cited by 62 · see citing works

Post-translational Modifications of Opioid Receptors

Duarte, M. L., & Devi, L. A. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.03.011 · Cited by 60 · see citing works

The spatial structure of cell signaling systems

Nussinov, R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/045004 · Cited by 49 · see citing works

Distinctive binding of three antagonistic peptides to the ephrin-binding pocket of the EphA4 receptor

Lamberto, I., Qin, H., Noberini, R., Premkumar, L., Bourgin, C., Riedl, S. J., Song, J., & Pasquale, E. B. (2012) · Biochemical Journal · doi:10.1042/bj20120408 · Cited by 48 · see citing works

FishPhyloMaker: An R package to generate phylogenies for ray-finned fishes

Nakamura, G., Richter, A., & Soares, B. E. (2021) · Ecological Informatics · doi:10.1016/j.ecoinf.2021.101481 · Cited by 44 · see citing works

Oligomerization and nanocluster organization render specificity

Nussinov, R., Jang, H., & Tsai, C. (2014) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12124 · Cited by 44 · see citing works

Elastin-inspired supramolecular hydrogels: a multifaceted extracellular matrix protein in biomedical engineering

Sharma, A., Sharma, P., & Roy, S. (2021) · Soft Matter · doi:10.1039/d0sm02202k · Cited by 44 · see citing works

The effect of aged microglia on synaptic impairment and its relevance in neurodegenerative diseases

Triviño, J. J., & von Bernhardi, R. (2021) · Neurochemistry International · doi:10.1016/j.neuint.2021.104982 · Cited by 43 · see citing works

Oncogenic mutations weaken the interactions that stabilize the p110α‐p85α heterodimer in phosphatidylinositol 3‐kinase α

Echeverria, I., Liu, Y., Gabelli, S. B., & Amzel, L. M. (2015) · FEBS Journal · doi:10.1111/febs.13365 · Cited by 41 · see citing works

Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study

Wang, W., Ye, W., Yu, Q., Jiang, C., Zhang, J., Luo, R., & Chen, H. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp4010967 · Cited by 41 · see citing works

Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

Fornili, A., Pandini, A., Lu, H., & Fraternali, F. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400486p · Cited by 38 · see citing works

cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions

Oliwa, T., & Shen, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv252 · Cited by 34 · see citing works

A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

Glanzer, J. G., Carnes, K. A., Soto, P., Liu, S., Parkhurst, L. J., & Oakley, G. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1291 · Cited by 33 · see citing works

Evolutionary Conserved Positions Define Protein Conformational Diversity

Saldaño, T. E., Monzón, A. M., Parisi, G. D., & Fernández-Alberti, S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004775 · Cited by 32 · see citing works

Compensatory Evolution and the Origins of Innovations

Rajon, É., & Masel, J. (2013) · Genetics · doi:10.1534/genetics.112.148627 · Cited by 32 · see citing works

Phylogeny of the family Aglajidae (Pilsbry, 1895) (Heterobranchia: Cephalaspidea) inferred from mtDNA and nDNA

Camacho-García, Y. E., Ornelas‐Gatdula, E., Gosliner, T. M., & Valdés, Á. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.11.010 · Cited by 31 · see citing works

CoDNaS: a database of conformational diversity in the native state of proteins

Monzón, A. M., Juritz, E., Fornasari, M. S., & Parisi, G. D. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt405 · Cited by 30 · see citing works

Ensembles in solution as a new paradigm for antibody structure prediction and design

Fernández‐Quintero, M. L., Georges, G. J., Varga, J. M., & Liedl, K. R. (2021) · mAbs · doi:10.1080/19420862.2021.1923122 · Cited by 30 · see citing works

Inhibition of Nonfunctional Ras

Nussinov, R., Jang, H., Gürsoy, A., Keskin, Ö., & Gaponenko, V. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2020.12.012 · Cited by 29 · see citing works

Dynamic conformational switching in the chemokine ligand is essential for G-protein-coupled receptor activation

Joseph, P. R. B., Sawant, K. V., Isley, A., Pedroza, M., Garofalo, R., Richardson, R. M., & Rajarathnam, K. (2013) · Biochemical Journal · doi:10.1042/bj20130148 · Cited by 26 · see citing works

Homology modeling in a dynamical world

Monzón, A. M., Zea, D. J., Marino‐Buslje, C., & Parisi, G. D. (2017) · Protein Science · doi:10.1002/pro.3274 · Cited by 26 · see citing works

Prediction of Multi-Type Membrane Proteins in Human by an Integrated Approach

Huang, G., Zhang, Y., Chen, L., Zhang, N., Huang, T., & Cai, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093553 · Cited by 20 · see citing works

Molecular Motions as a Drug Target: Mechanistic Simulations of Anthrax Toxin Edema Factor Function Led to the Discovery of Novel Allosteric Inhibitors

Laine, É., Martı́nez, L., Ladant, D., Malliavin, T. E., & Blondel, A. (2012) · Toxins · doi:10.3390/toxins4080580 · Cited by 20 · 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

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

EphA4‐deleted microenvironment regulates cancer development and leukemoid reaction of the isografted 4T1 murine breast cancer via reduction of an IGF 1 signal

Jing, X., Sonoki, T., Miyajima, M., Sawada, T., Terada, N., Takemura, S., & Sakaguchi, K. (2016) · Cancer Medicine · doi:10.1002/cam4.670 · Cited by 15 · see citing works

Using Local States To Drive the Sampling of Global Conformations in Proteins

Pandini, A., & Fornili, A. (2016) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5b00992 · Cited by 14 · see citing works

Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations

Pastor, N., & Amero, C. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00306 · Cited by 14 · see citing works

Addressing the Role of Conformational Diversity in Protein Structure Prediction

Palópoli, N., Monzón, A. M., Parisi, G. D., & Fornasari, M. S. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154923 · Cited by 13 · see citing works

The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis

Yuan, H., & Koelle, K. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0204 · Cited by 13 · see citing works

Network analysis of dynamically important residues in protein structures mediating ligand-binding conformational changes

Saldaño, T. E., Tosatto, S. C. E., Parisi, G. D., & Fernández-Alberti, S. (2019) · European Biophysics Journal · doi:10.1007/s00249-019-01384-1 · Cited by 12 · see citing works

Optimization of Compound Ranking for Structure‐Based Virtual Ligand Screening Using an Established FRED –Surflex Consensus Approach

Du, J., Bleylevens, I. W. M., Bitorina, A. V., Wichapong, K., & Nicolaes, G. A. F. (2013) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12202 · Cited by 11 · see citing works

Investigation of the interactions between the EphB2 receptor and SNEW peptide variants

Ma, B., Kolb, S., Diprima, M., Karna, M., Tosato, G., Yang, Q., Huang, Q., & Nussinov, R. (2014) · Growth Factors · doi:10.3109/08977194.2014.985786 · Cited by 10 · see citing works

Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

Hu, Q., Williams, M. T., Shulgina, I., Fossum, C. J., Weeks, K. M., Adams, L. M., Reinhardt, C. R., Musier‐Forsyth, K., Hati, S., & Bhattacharyya, S. (2020) · ACS Catalysis · doi:10.1021/acscatal.0c02381 · Cited by 7 · see citing works

Exploring Conformational Space with Thermal Fluctuations Obtained by Normal-Mode Analysis

Saldaño, T. E., Freixas, V. M., Tosatto, S. C. E., Parisi, G. D., & Fernández-Alberti, S. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b01136 · Cited by 6 · see citing works

Mechanical variations in proteins with large-scale motions highlight the formation of structural locks

Sacquin‐Mora, S. (2018) · Journal of Structural Biology · doi:10.1016/j.jsb.2018.05.006 · Cited by 5 · see citing works

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure

Escobedo, N., Cahui, R. R. T., Caruso, G., Ríos, E. G., Hirsh, L., Monzón, A. M., Parisi, G. D., & Palópoli, N. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac627 · Cited by 5 · see citing works

Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins

Mamidi, A. S., & Surolia, A. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010661 · Cited by 4 · see citing works

A model based on minimotifs for classification of stable protein-protein complexes

Rueda, L. G., & Pandit, M. (2014) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb.2014.6845508 · Cited by 4 · see citing works

Characterizing the relation of functional and Early Folding Residues in protein structures using the example of aminoacyl-tRNA synthetases

Bittrich, S., Schroeder, M., & Labudde, D. (2018) · PLoS ONE · doi:10.1371/journal.pone.0206369 · Cited by 4 · see citing works

Probing the Structural Dynamics of the Plasmodium falciparum Tunneling-Fold Enzyme 6-Pyruvoyl Tetrahydropterin Synthase to Reveal Allosteric Drug Targeting Sites

Khairallah, A., Ross, C. J., & Bishop, Ö. T. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.575196 · Cited by 4 · see citing works

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins

Das, S., Bhadra, P., Ramakumar, S., & Pal, D. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00217 · Cited by 4 · see citing works

In Search of a Dynamical Vocabulary: A Pipeline to Construct a Basis of Shared Traits in Large-Scale Motions of Proteins

Tarenzi, T., Mattiotti, G., Rigoli, M., & Potestio, R. (2022) · Applied Sciences · doi:10.3390/app12147157 · Cited by 3 · see citing works

A Computational Approach to Characterize the Protein S-Mer Tyrosine Kinase (PROS1-MERTK) Protein-Protein Interaction Dynamics

Djulbegovic, M. B., Gonzalez, D. J. T., Laratelli, L., Antonietti, M., Uversky, V. N., Shields, C. L., & Karp, C. L. (2024) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-024-01582-5 · Cited by 3 · see citing works

Multi-state Targeting Machinery Govern the Fidelity and Efficiency of Protein Localization

Yang, M., Pang, X., & Han, K. (2013) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-02970-2_16 · Cited by 3 · see citing works

Association Between the PIK3CA Ile391Met Polymorphism and the Risk of Breast Cancer in an Iranian Population

Ahmadi, S., Ramezani, S., Ghafouri, H., Hosseini, S. M., Najafi, A., & Keihan, A. H. (2018) · Journal of Applied Biotechnology Reports · doi:10.29252/jabr.01.01.02 · Cited by 3 · see citing works

Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulationsPreprint

Roy, A., Lim, L., Srivastava, S., & Song, J. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/078113 · Cited by 3 · see citing works

SAGERank: inductive learning of protein–protein interaction from antibody–antigen recognition

Sun, C., Li, X., Xu, H., Tang, Y., ganggang, B., Wang, Y., & Ma, B. (2025) · Chemical Science · doi:10.1039/d5sc03707g · Cited by 2 · see citing works

Antagonistic Control of Genetic Circuit Performance for Rapid Analysis of Targeted Enzyme Activity in Living Cells

Kwon, K. K., Kim, H., Yeom, S., Rha, E., Lee, J., Lee, H., Lee, D., & Lee, S. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.599878 · Cited by 2 · see citing works

Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening

Romero, J. A. L., & Kolmar, H. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3279-6_14 · Cited by 1 · see citing works

A protein engineering approach toward understanding FKBP51 conformational dynamics and mechanisms of ligand binding

Romero, J. A. L., Meyners, C., Rupp, N., Hausch, F., & Kolmar, H. (2023) · Protein Engineering Design and Selection · doi:10.1093/protein/gzad014 · Cited by 1 · see citing works

Conformational Heterogeneity and Catalytic Promiscuity in Glutathione Transferases

Honaker, M. T. (2012) · ResearchWorks at the University of Washington (University of Washington)

Protein token: a dynamic unit in protein interactionsPreprint

Luo, S.-W., Jiang, Y., Liang, Z., & Wu, J. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1809.10458

Mass Spectrometry-Based Footprinting Strategies for GPCR Structure Analysis

Jin, Y. T., Roberts, R., Smith, C. G., & Sun, J. (2026) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.6c00278

Application of in-silico approaches to cardiovascular disease

Du, J. (2014) · doi:10.26481/dis.20141008jd

bidirectional signal transduction

Nussinov, R., & Ma, B. (2013)

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

Crystal structure of the ligand-binding domain of the promiscuous EphA4 receptor reveals two distinct conformations

Singla, N., Goldgur, Y., Xu, K. Y., Paavilainen, S., Nikolov, D. B., & Himanen, J. P. (2010) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2010.07.109 · Cited by 30 · 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

Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR andMD simulations. PLoS One. 2013; 8: e74040. doi: 10.1371/journal.pone.0074040 PMID: 24086308

Huan, X., Shi, J., Lim, L. Z., Mitra, S., Zhu, W., Qin, H., Pasquale, E. B., & Song, J. (2016)