Folding funnels and binding mechanisms

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Serotonin and Melatonin Show Different Modes of Action on Aβ42 Protofibril Destabilization

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Binding and folding: in search of intramolecular chaperone-like building block fragments

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Local Fluctuations and Conformational Transitions in Proteins

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Metazoan parasites of swordfish, Xiphias gladius (Pisces: Xiphiidae) from the Atlantic Ocean: implications for host stock identification

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

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A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex

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Structural, Energetic, and Dynamic Aspects of Ligand–Receptor Interactions

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Physicochemical bases for protein folding, dynamics, and protein-ligand binding

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Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces

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Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model

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Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase

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Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

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Intrinsically disordered proteins: Chronology of a discovery

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Recent Progress in Antibody Epitope Prediction

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Blinking fluorophores: what do they tell us about protein dynamics?

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Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants

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Protein conformation as a regulator of cell–matrix adhesion

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Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations

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Protein charge and mass contribute to the spatio‐temporal dynamics of protein–protein interactions in a minimal proteome

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Dynamic multiprotein assemblies shape the spatial structure of cell signaling

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From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

Akhter, N., & Shehu, A. (2018) · Molecules · doi:10.3390/molecules23010216 · Cited by 37

Do protein–protein interaction databases identify moonlighting proteins?

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Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design

Berezovsky, I. N., & Nussinov, R. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167751 · Cited by 39

Polymorphic C-terminal β-Sheet Interactions Determine the Formation of Fibril or Amyloid β-derived Diffusible Ligand-like Globulomer for the Alzheimer Aβ42 Dodecamer

Ma, B., & Nussinov, R. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.133488 · Cited by 36

Solution NMR views of dynamical ordering of biomacromolecules

Ikeya, T., Ban, D., Lee, D., Ito, Y., Kato, K., & Griesinger, C. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.08.020 · Cited by 37

Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots

Stachowski, T. R., & Fischer, M. M. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c00708 · Cited by 35

The role of allostery in the ubiquitin–proteasome system

Liu, J., & Nussinov, R. (2012) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2012.742856 · Cited by 34

Arginine Kinase: Joint Crystallographic and NMR RDC Analyses Link Substrate-Associated Motions to Intrinsic Flexibility

Niu, X., Bruschweiler‐Li, L., Davulcu, O., Skalicky, J. J., Brüschweiler, R., & Chapman, M. S. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.11.007 · Cited by 37

Autoinhibition can identify rare driver mutations and advise pharmacology

Nussinov, R., Tsai, C., & Jang, H. (2019) · The FASEB Journal · doi:10.1096/fj.201901341r · Cited by 35

Engineering an Allosteric Control of Protein Function

Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33

Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics

Son, A., Kim, W., Park, J., Lee, W., Lee, Y., Choi, S., & Kim, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25179725 · Cited by 39

Improving Virtual Screening Performance against Conformational Variations of Receptors by Shape Matching with Ligand Binding Pocket

Lee, H. S., Lee, C.-S., Kim, J. S., Kim, D. H., & Choe, H. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9002365 · Cited by 34

Optimal Drug Cocktail Design: Methods for Targeting Molecular Ensembles and Insights from Theoretical Model Systems

Radhakrishnan, M. L., & Tidor, B. (2008) · Journal of Chemical Information and Modeling · doi:10.1021/ci700452r · Cited by 34

Combining NMR and Molecular Dynamics Studies for Insights into the Allostery of Small GTPase–Protein Interactions

Zhang, L., Bouguet‐Bonnet, S., & Buck, M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-334-9_13 · Cited by 34

Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

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The Catalytic Tyr-9 of Glutathione S-Transferase A1-1 Controls the Dynamics of the C terminus

Nieslanik, B. S., & Atkins, W. M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m002083200 · Cited by 35

How do dynamic cellular signals travel long distances?

Nussinov, R. (2011) · Molecular BioSystems · doi:10.1039/c1mb05205e · Cited by 34

Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations

Allen, B. K., Mehta, S., Ember, S. W., Zhu, J.-Y., Schönbrunn, E., Ayad, N. G., & Schürer, S. C. (2017) · ACS Omega · doi:10.1021/acsomega.7b00553 · Cited by 33

Tunable order–disorder continuum in protein–DNA interactions

Munshi, S., Gopi, S., Asampille, G., Subramanian, S., Campos, L. A., Atreya, H. S., & Naganathan, A. N. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky732 · Cited by 34

Are Parallel Proliferation Pathways Redundant?

Nussinov, R., Tsai, C., & Jang, H. (2020) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2020.03.013 · Cited by 33

A Markov‐chain model description of binding funnels to enhance the ranking of docked solutions

Torchala, M., Moal, I. H., Chaleil, R. A. G., Agius, R., & Bates, P. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24369 · Cited by 33

Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins

Tsai, C., de Laureto, P. P., Fontana, A., & Nussinov, R. (2002) · Protein Science · doi:10.1110/ps.4100102 · Cited by 32

Intrinsically Disordered Proteins

Uversky, V. N. (2020) · Wiley eBooks · doi:10.1002/9781118681121.ch25 · Cited by 33

Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1

Ferraro, M., Moroni, E., Ippoliti, E., Rinaldi, S., Sànchez‐Martìn, C., Rasola, A., Pavarino, L. F., & Colombo, G. (2020) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c09742 · Cited by 32

Side-Chain Conformational Changes upon Protein–Protein Association

Ruvinsky, A. M., Kirys, T., Tuzikov, A. V., & Vakser, I. A. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.02.030 · Cited by 33

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Nussinov, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169044 · Cited by 34

From “fluctuation fit” to “conformational selection”: Evolution, rediscovery, and integration of a concept

Vértessy, B. G., & Orosz, F. (2010) · BioEssays · doi:10.1002/bies.201000068 · Cited by 33

Direct visualization reveals dynamics of a transient intermediate during protein assembly

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Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning

Xie, Z., Chen, J. C., & Wu, Y. (2017) · Scientific Reports · doi:10.1038/srep46622 · Cited by 32

Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

Ping, J., Hao, P., Li, Y., & Wang, J. (2013) · BioMed Research International · doi:10.1155/2013/628536 · Cited by 31

Free Energy Diagrams for Protein Function

Nussinov, R., & Tsai, C. (2014) · Chemistry & Biology · doi:10.1016/j.chembiol.2013.12.015 · Cited by 31

Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations

Koga, N., Kameda, T., Okazaki, K.-I., & Takada, S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904756106 · Cited by 31

Conformational selection or induced fit for Brinker and DNA recognition

Fang, Q., Jiang, Y., Chen, Y., Wu, M., Yan, G., Ye, W., Li, Y., Zhang, J., & Chen, H. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00701c · Cited by 31

Experimental and computational models to understand protein-ligand, metal-ligand and metal-DNA interactions pertinent to targeted cancer and other therapies

Patil, V. M., Gupta, S. P., Masand, N., & Balasubramanian, K. (2024) · European Journal of Medicinal Chemistry Reports · doi:10.1016/j.ejmcr.2024.100133 · Cited by 33

Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin

Kahler, U., Kamenik, A. S., Waibl, F., Kraml, J., & Liedl, K. R. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.06.032 · Cited by 28

Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery

Fleishman, S. J., & Horovitz, A. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167007 · Cited by 28

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 31

Mechanism of activation and the rewired network: New drug design concepts

Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30

Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations

Paul, F., Noé, F., & Weikl, T. R. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b12146 · Cited by 31

Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality

Uversky, V. N. (2023) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2023.11.001 · Cited by 31

Discorhabdin N, a South African Natural Compound, for Hsp72 and Hsc70 Allosteric Modulation: Combined Study of Molecular Modeling and Dynamic Residue Network Analysis

Amusengeri, A., & Bishop, Ö. T. (2019) · Molecules · doi:10.3390/molecules24010188 · Cited by 28

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

Kidera, A., Moritsugu, K., Ekimoto, T., & Ikeguchi, M. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167324 · Cited by 29

Induced fit for mRNA/TIS11d complex

Fang, Q., Chen, Y., Li, Y., & Chen, H. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3224126 · Cited by 29

A Mechanistic View of the Role of E3 in Sumoylation

Tozluoǧlu, M., Karaca, E., Nussinov, R., & Haliloǧlu, T. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000913 · Cited by 29

Influence of glycosidic linkage on the nature of carbohydrate binding in β-prism I fold lectins: An X-ray and molecular dynamics investigation on banana lectin–carbohydrate complexes

Sharma, A., & Vijayan, M. (2010) · Glycobiology · doi:10.1093/glycob/cwq128 · Cited by 30

Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis

Pusuluk, O., Farrow, T., Cemsinan Deliduman, B., Burnett, K., & Vedral, V. (2018) · Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rspa.2018.0037 · Cited by 28

Networks of Networks: An Essay on Multi-Level Biological Organization

Uversky, V. N., & Giuliani, A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.706260 · Cited by 28

Cholera Toxin B Subunits Assemble into Pentamers - Proposition of a Fly-Casting Mechanism

Zrimi, J., Ling, A. N., Giri-Rachman, E. A., Feverati, G., & Lesieur, C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015347 · Cited by 30

Arrestins: structural disorder creates rich functionality

Gurevich, V. V., Gurevich, E. V., & Uversky, V. N. (2018) · Protein & Cell · doi:10.1007/s13238-017-0501-8 · Cited by 29

The size of the intermolecular energy funnel in protein–protein interactions

Hunjan, J. S., Tovchigrechko, A., Gao, Y. D., & Vakser, I. A. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21930 · Cited by 28

PCDB: a database of protein conformational diversity

Juritz, E., Fernández-Alberti, S., & Parisi, G. D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1181 · Cited by 28

Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations

Uehara, S., & Tanaka, S. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00791 · Cited by 28

Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?

Ma, B., Tsai, C., Pan, Y., & Nussinov, R. (2010) · ACS Chemical Biology · doi:10.1021/cb900293a · Cited by 28

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

Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics

Fernández‐Quintero, M. L., Kroell, K. B., Bacher, L. M., Loeffler, J. R., Quoika, P. K., Georges, G. J., Bujotzek, A., Kettenberger, H., & Liedl, K. R. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.675655 · Cited by 27

Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures

Danielson, M. L., Desai, P. V., Mohutsky, M. A., Wrighton, S. A., & Lill, M. A. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.05.067 · Cited by 28

Minimal ensembles of side chain conformers for modeling protein–protein interactions

Beglov, D., Hall, D. R., Brenke, R., Shapovalov, M. V., Dunbrack, R. L., Kozakov, D., & Vajda, S. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23222 · Cited by 28

Probing protein ensemble rigidity and hydrogen–deuterium exchange

Sljoka, A., & Wilson, D. (2013) · Physical Biology · doi:10.1088/1478-3975/10/5/056013 · Cited by 27

Rapid Evolutionary Dynamics of Structural Disorder as a Potential Driving Force for Biological Divergence in Flaviviruses

Ortiz, J. F., MacDonald, M. L., Masterson, P., Uversky, V. N., & Siltberg-Liberles, J. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt026 · Cited by 27

The Too Many Faces of PD-L1: A Comprehensive Conformational Analysis Study

Ahmed, M., & Barakat, K. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00655 · Cited by 27

T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions

Fernández‐Quintero, M. L., Pomarici, N. D., Loeffler, J. R., Seidler, C. A., & Liedl, K. R. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01440 · Cited by 28

Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK

Kong, X., Sun, H., Pan, P., Zhu, F., Chang, S., Xu, L., Li, Y., & Hou, T. (2018) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp08241j · Cited by 26

Intrinsic Domain and Loop Dynamics Commensurate with Catalytic Turnover in an Induced-Fit Enzyme

Davulcu, O., Flynn, P. F., Chapman, M. S., & Skalicky, J. J. (2009) · Structure · doi:10.1016/j.str.2009.08.014 · Cited by 26

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 27

Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes

Ma, B., Zhao, J., & Nussinov, R. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.05.040 · Cited by 26

Specificity and stability of transient protein–protein interactions

Vishwanath, S., Sukhwal, A., Sowdhamini, R., & Srinivasan, N. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.12.010 · Cited by 27

Protein–Protein Interaction Interfaces and their Functional Implications

Schreiber, G. (2020) · Royal Society of Chemistry eBooks · doi:10.1039/9781788016544-00001 · Cited by 29

Protein flexibility and electrostatic interactions

Kumar, S., Wolfson, H. J., & Nussinov, R. (2001) · IBM Journal of Research and Development · doi:10.1147/rd.453.0499 · Cited by 25

The Structure of Lombricine Kinase

Bush, D. J., Kirillova, O. V., Clark, S. A., Davulcu, O., Fabiola, F., Xie, Q., Somasundaram, T., Ellington, W. R., & Chapman, M. S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.202796 · Cited by 25

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein–protein binding

Kirys, T., Ruvinsky, A. M., Tuzikov, A. V., & Vakser, I. A. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24103 · Cited by 25

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding

Fuchs, J. E., Waldner, B. J., Huber, R. G., von Grafenstein, S., Krämer, C., & Liedl, K. R. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct500633u · Cited by 24

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization

Zhan, C., Qi, R., Wei, G., Guven‐Maiorov, E., Nussinov, R., & Ma, B. (2016) · Protein Engineering Design and Selection · doi:10.1093/protein/gzw033 · Cited by 24

A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic

Shehu, A., & Plaku, E. (2016) · Journal of Artificial Intelligence Research · doi:10.1613/jair.5040 · Cited by 25

Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes

Fernández‐Quintero, M. L., Loeffler, J. R., Waibl, F., Kamenik, A. S., Hofer, F., & Liedl, K. R. (2019) · Protein Engineering Design and Selection · doi:10.1093/protein/gzaa014 · Cited by 25

An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid

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Apo Adenylate Kinase Encodes Its Holo Form: A Principal Component and Varimax Analysis

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