Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works

Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model

Atılgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, Ö., & Bahar, İ. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)76033-x · Cited by 1,638 · see citing works

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

Tirion, M. M. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.1905 · Cited by 1,617 · see citing works

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

Bahar, İ., Atılgan, A. R., & Erman, B. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00024-2 · Cited by 1,377 · see citing works

A Perspective on Enzyme Catalysis

Benkovic, S. J., & Hammes‐Schiffer, S. (2003) · Science · doi:10.1126/science.1085515 · Cited by 1,281 · see citing works

Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin.

Roe, S. M., Prodromou, C., O'Brien, R., Ladbury, J. E., Piper, P. W., & Pearl, L. H. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm980403y · Cited by 1,004 · see citing works

Conformational change of proteins arising from normal mode calculations

Tama, F., & Sanejouand, Y. (2001) · Protein Engineering Design and Selection · doi:10.1093/protein/14.1.1 · Cited by 895 · see citing works

Gaussian Dynamics of Folded Proteins

Haliloǧlu, T., Bahar, İ., & Erman, B. (1997) · Physical Review Letters · doi:10.1103/physrevlett.79.3090 · Cited by 806 · see citing works

Enzyme Dynamics During Catalysis

Eisenmesser, E. Z., Bosco, D. A., Akke, M., & Kern, D. (2002) · Science · doi:10.1126/science.1066176 · Cited by 732 · see citing works

Dynamics of a small globular protein in terms of low-frequency vibrational modes.

Gō, N., Noguti, T., & Nishikawa, T. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.12.3696 · Cited by 729 · see citing works

Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme

Levitt, M., Sander, C., & Stern, P. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90230-x · Cited by 728 · see citing works

ACE2 X-Ray Structures Reveal a Large Hinge-bending Motion Important for Inhibitor Binding and Catalysis

Towler, P., Staker, B. L., Prasad, S. G., Menon, S., Tang, J., Parsons, T. F., Ryan, D., Fisher, M., Williams, D., Dales, N. A., et al. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311191200 · Cited by 699 · see citing works

DYNAMICS OF PROTEINS: ELEMENTS AND FUNCTION

Kurplus, M., & McCammon, J. A. (1983) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.52.070183.001403 · Cited by 686 · see citing works

Statistical thermodynamics of random networks

Flory, P. J. (1976) · Proceedings of the Royal Society of London A Mathematical and Physical Sciences · doi:10.1098/rspa.1976.0146 · Cited by 645 · see citing works

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

Porter, C. T. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh028 · Cited by 605 · see citing works

Analysis of Catalytic Residues in Enzyme Active Sites

Bartlett, G. J., Porter, C. T., Borkakoti, N., & Thornton, J. M. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)01036-7 · Cited by 589 · see citing works

Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase

Kohen, A., Cannio, R., Bartolucci, S., Klinman, J. P., & Klinman, J. P. (1999) · Nature · doi:10.1038/20981 · Cited by 582 · see citing works

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

Wolf‐Watz, M., Thai, V., Henzler‐Wildman, K. A., Hadjipavlou, G., Eisenmesser, E. Z., & Kern, D. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb821 · Cited by 494 · see citing works

Investigating protein dynamics in collective coordinate space

Kitao, A., & Gō, N. (1999) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(99)80023-2 · Cited by 475 · see citing works

Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme

Banks, R. D., Blake, C. C. F., Evans, P. R., Haser, R., Rice, D. W., Hardy, G. W., Merrett, M., & Phillips, A. W. (1979) · Nature · doi:10.1038/279773a0 · Cited by 451 · see citing works

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

Bahar, İ., Atılgan, A. R., Demirel, M. C., & Erman, B. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.2733 · Cited by 442 · see citing works

Structure of Human Methionine Aminopeptidase-2 Complexed with Fumagillin

Liu, S., Widom, J., Kemp, C. W., Crews, C. M., & Clardy, J. (1998) · Science · doi:10.1126/science.282.5392.1324 · Cited by 440 · see citing works

The hinge-bending mode in lysozyme

McCammon, J. A., Gelin, B. R., Karplus, M., & Wolynes, P. G. (1976) · Nature · doi:10.1038/262325a0 · Cited by 379 · see citing works

The Role of Dynamics in Enzyme Activity

Daniel, R. M., Dunn, R. V., Finney, J., & Smith, J. C. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142445 · Cited by 360 · see citing works

Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes

Matthews, D. A., Dragovich, P. S., Webber, S. E., Fuhrman, S. A., Patick, A. K., Zalman, L. S., Hendrickson, T. F., Love, R. A., Prins, T. J., Marakovits, J. T., et al. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11000 · Cited by 319 · see citing works

The Glass Transition

Donth, E.-J. (2001) · Springer series in materials science · doi:10.1007/978-3-662-04365-3 · Cited by 282 · see citing works

Dynamics of Proteins in Crystals: Comparison of Experiment with Simple Models

Kundu, S., Melton, J. S., Sorensen, D. C., & Phillips, G. N. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75203-x · Cited by 254 · see citing works

The ‘glass transition’ in protein dynamics: what it is, why it occurs, and how to exploit it

Ringe, D., & Petsko, G. A. (2003) · Biophysical Chemistry · doi:10.1016/s0301-4622(03)00096-6 · Cited by 251 · see citing works

Structure of Recombinant Human CPP32 in Complex with the Tetrapeptide Acetyl-Asp-Val-Ala-Asp Fluoromethyl Ketone

Mittl, P. R. E., Marco, S. D., Krebs, J., Bai, X., Karanewsky, D. S., Priestle, J. P., Tomaselli, K. J., & Grütter, M. G. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.10.6539 · Cited by 250 · see citing works

Detoxification of environmental mutagens and carcinogens: Structure, mechanism, and evolution of liver epoxide hydrolase

Argiriadi, M. A., Morisseau, C. H. P., Hammock, B. D., & Christianson, D. W. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.19.10637 · Cited by 228 · see citing works

Discriminating between homodimeric and monomeric proteins in the crystalline state

Ponstingl, H., Henrick, K., & Thornton, J. M. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001001)41:1 · Cited by 226 · see citing works

Collective Motions in HIV-1 Reverse Transcriptase: Examination of Flexibility and Enzyme Function

Bahar, İ., Erman, B., Jernigan, R. L., Atılgan, A. R., & Covell, D. G. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2371 · Cited by 201 · see citing works

Structure of the Complex between the Antibiotic Cerulenin and Its Target, β-Ketoacyl-Acyl Carrier Protein Synthase

Moche, M., Schneider, G., Edwards, P. C., Dehesh, K., & Lindqvist, Y. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.10.6031 · Cited by 200 · see citing works

Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T↔R2 Transition

Xu, C., Tobi, D., & Bahar, İ. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.08.027 · Cited by 198 · see citing works

The structures of human glutathione transferase P1-1 in complex with glutathione and various inhibitors at high resolution

Oakley, A. J., Bello, M. L., Battistoni, A., Ricci, G., Rossjohn, J., Villar, H. O., & Parker, M. W. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1364 · Cited by 189 · see citing works

The allosteric mechanism of the chaperonin GroEL: A dynamic analysis

Ma, J., & Karplus, M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.15.8502 · Cited by 185 · see citing works

Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli

Wilce, M. C. J., Bond, C. S., Dixon, N. E., Freeman, H. C., Guss, J. M., Lilley, P. E., & Wilce, M. C. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.7.3472 · Cited by 182 · see citing works

Hinge‐mediated dimerization of SMC protein is essential for its dynamic interaction with DNA

Hirano, T., & Hirano, T. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf575 · Cited by 179 · see citing works

The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme

Freire, E. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.10118 · Cited by 177 · see citing works

Sugar Ring Distortion in the Glycosyl-Enzyme Intermediate of a Family G/11 Xylanase ,

Sidhu, G., Withers, S. G., Nguyen, N. T., McIntosh, L. P., Ziser, L., & Brayer, G. D. (1999) · Biochemistry · doi:10.1021/bi982946f · Cited by 176 · see citing works

Using A Neural Network and Spatial Clustering to Predict the Location of Active Sites in Enzymes

Gutteridge, A., Bartlett, G. J., & Thornton, J. M. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00515-1 · Cited by 175 · see citing works

How to describe protein motion without amino acid sequence and atomic coordinates

Ming, D., Kong, Y., Lambert, M. A., Huang, Z. X., & Ma, J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082148899 · Cited by 167 · see citing works

Dynamics and function of proteins: The search for general concepts

Frauenfelder, H., & McMahon, B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.4795 · Cited by 141 · see citing works

Lowering the Entropic Barrier for Binding Conformationally Flexible Inhibitors to Enzymes,

Khan, A. R., Parrish, J. C., Fraser, M. E., Smith, W. W., Bartlett, P. A., & James, M. N. G. (1998) · Biochemistry · doi:10.1021/bi9821364 · Cited by 133 · see citing works

iGNM: a database of protein functional motions based on Gaussian Network Model

Yang, L.-W., Liu, X., Jursa, C. J., Holliman, M., Rader, A. J., Karimi, H. A., & Bahar, İ. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti469 · Cited by 119 · see citing works

Engineering of Cyclodextrin Product Specificity and pH Optima of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1

Wind, R. D., Uitdehaag, J. C. M., Buitelaar, R. M., Dijkstra, B. W., & Dijkhuizen, L. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.10.5771 · Cited by 118 · see citing works

Protein Motions Promote Catalysis

Tousignant, A., & Pelletier, J. N. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.06.007 · Cited by 116 · see citing works

Molecular Dynamics Simulations of Peptides and Proteins with Amplified Collective Motions

Zhang, Z., Shi, Y., & Liu, H. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)75090-5 · Cited by 114 · see citing works

Inhibition of β-lactamase by clavulanate

Chen, C. C. H., & Herzberg, O. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90472-v · Cited by 105 · see citing works

Structure-based identification of a ricin inhibitor

Yan, X., Hollis, T., Svinth, M., Day, P., Monzingo, A. F., Milne, G. W. A., & Robertus, J. D. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0865 · Cited by 95 · see citing works

Structures of murine carbonic anhydrase IV and human carbonic anhydrase II complexed with brinzolamide: Molecular basis of isozyme‐drug discrimination

Stams, T., Chen, Y., Christianson, D. W., Boriack‐Sjodin, P. A., Hurt, J. D., Laipis, P. J., Silverman, D. N., Liao, J. C., May, J. A., & Dean, T. R. (1998) · Protein Science · doi:10.1002/pro.5560070303 · Cited by 95 · see citing works

Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data

Temiz, N. A., Meirovitch, E., & Bahar, İ. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20226 · Cited by 92 · see citing works

Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl−Prolyl Cis−Trans Isomerization Activity of Cyclophilin A

Agarwal, P. K., Geist, A., & Gorin, A. A. (2004) · Biochemistry · doi:10.1021/bi0495228 · Cited by 88 · see citing works

Three-Dimensional Structure of Escherichia coli Dihydrodipicolinate Reductase in Complex with NADH and the Inhibitor 2,6-Pyridinedicarboxylate,

Scapin, G., Reddy, S. G., Zheng, R., & Blanchard, J. S. (1997) · Biochemistry · doi:10.1021/bi9719915 · Cited by 87 · see citing works

Hydrophilic Peptides Derived from the Transframe Region of Gag-Pol Inhibit the HIV-1 Protease

Louis, J. M., Dyda, F., Nashed, N. T., Kimmel, A. R., & Davies, D. R. (1998) · Biochemistry · doi:10.1021/bi972059x · Cited by 86 · see citing works

Crystal structure of an actinidin-E-64 complex

Varughese, K. I., Su, Y., Cromwell, D., Hasnain, S., & Xuong, N. H. (1992) · Biochemistry · doi:10.1021/bi00137a012 · Cited by 86 · see citing works

Characteristics of nearly dry enzymes in organic solvents: implications for biocatalysis in the absence of water

Clark, D. S. (2004) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2004.1506 · Cited by 86 · see citing works

Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor

Lubkowski, J. T., Yang, F., Alexandratos, J. N., Wlodawer, A., Zhao, H., Burke, T. R., Neamati, N., Pommier, Y. G., Merkel, G. W., & Skalka, A. M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.4831 · Cited by 84 · see citing works

Inhibitor binding alters the directions of domain motions in HIV‐1 reverse transcriptase

Temiz, N. A., & Bahar, İ. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10183 · Cited by 80 · see citing works

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein

Pang, A., Arinaminpathy, Y., Sansom, M. S. P., & Biggin, P. C. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)00866-4 · Cited by 72 · see citing works

Domain movements in human fatty acid synthase by quantized elastic deformational model

Ming, D., Kong, Y., Wakil, S. J., Brink, J., & Ma, J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112222299 · Cited by 70 · see citing works

A Moving Story

Falke, J. J. (2002) · Science · doi:10.1126/science.1069823 · Cited by 66 · see citing works

Structures of native and complexed complement factor D: implications of the atypical his57 conformation and self-inhibitory loop in the regulation of specific serine protease activity

Hua, J., Babu, Y. S., Moore, D., Kilpatrick, J. M., Liu, X., Volanakis, J. E., & Narayana, S. V. L. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2089 · Cited by 65 · see citing works

Correlations of the Basicity of His 57 with Transition State Analogue Binding, Substrate Reactivity, and the Strength of the Low-Barrier Hydrogen Bond in Chymotrypsin

Lin, J. C., Cassidy, C. S., & Frey, P. A. (1998) · Biochemistry · doi:10.1021/bi980278s · Cited by 62 · see citing works

Insights into the Acylation Mechanism of Class A β-Lactamases from Molecular Dynamics Simulations of the TEM-1 Enzyme Complexed with Benzylpenicillin

Díaz, N., Sordo, T. L., Merz, K. M., & Suárez, D. (2002) · Journal of the American Chemical Society · doi:10.1021/ja027704o · Cited by 59 · see citing works

Three‐dimensional structures of glycolate oxidase with bound active‐site inhibitors

Stenberg, K., & Lindqvist, Y. (1997) · Protein Science · doi:10.1002/pro.5560060506 · Cited by 59 · see citing works

Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide

Zhao, H., Tang, L., Wang, X., Zhou, Y.-C., & Lin, Z. (1998) · Toxicon · doi:10.1016/s0041-0101(97)00169-4 · Cited by 55 · see citing works

Three-Dimensional Structure of Escherichia coli Dihydrodipicolinate Reductase

Scapin, G., Blanchard, J. S., & Sacchettini, J. C. (1995) · Biochemistry · doi:10.1021/bi00011a003 · Cited by 55 · see citing works

Glycine Insertion in the Hinge Region of Lactose Repressor Protein Alters DNA Binding

Falcon, C. M., & Matthews, K. S. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.43.30849 · Cited by 55 · see citing works

Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction

Luo, J., & Bruice, T. C. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405502101 · Cited by 39 · see citing works

Catalytic Domain Structure of Vampire Bat Plasminogen Activator: A Molecular Paradigm for Proteolysis without Activation Cleavage

Renatus, M., Stubbs, M. T., Huber, R., Bringmann, P., Donner, P., Schleuning, W.-D. D., & Bode, W. (1997) · Biochemistry · doi:10.1021/bi971129x · Cited by 39 · see citing works

Mining frequent patterns in protein structures: a study of protease families

Chen, S.-C., & Bahar, İ. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth912 · Cited by 39 · see citing works

The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase 1 1Edited by P. E. Wright

Xiang, J., Sun, J., & Sampson, N. S. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4536 · Cited by 36 · see citing works

Crystal structure of the complex of human α‐thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin—2 and hirutonin—6

Zdanov, A. S., Wu, S., DiMaio, J., Konishi, Y., Li, Y., Wu, X., Edwards, B. F. P., Martin, P. D., & Cygler, M. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170304 · Cited by 34 · see citing works

Crystal structure of subtilisin DY, a random mutant of subtilisin Carlsberg

Eschenburg, S., Genov, N. C., Peters, K., FITTKAU, S., Stoeva, S., Wilson, K. S., & Betzel, C. (1998) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.1998.2570309.x · Cited by 26 · see citing works

Interdomain Interactions in Hinge-Bending Transitions

Sinha, N., Kumar, S., & Nussinov, R. (2001) · Structure · doi:10.1016/s0969-2126(01)00687-6 · Cited by 22 · see citing works

Hinge-bending motions in annexins: molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I

Cregut, D., Drin, G., Liautard, J., & Chiche, L. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.10.891 · Cited by 22 · see citing works

Tunnel vision

Ringe, D., & Petsko, G. A. (1999) · Nature · doi:10.1038/20819 · Cited by 21 · see citing works

Coarse-grained normal mode analysis in structural biology

Bahar, İ., & Rader, A. J. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.08.007 · Cited by 732 · see citing works

Unusual biophysics of intrinsically disordered proteins.

Uversky, V. (2013) · Biochimica et Biophysica Acta · doi:10.1016/j.bbapap.2012.12.008 · Cited by 536 · see citing works

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

Bahar, İ., Lezon, T. R., Bakan, A., & Shrivastava, I. H. (2009) · Chemical Reviews · doi:10.1021/cr900095e · Cited by 534 · see citing works

Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability

Sun, Z., Liu, Q., Qu, G., Feng, Y. F., & Reetz, M. T. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00290 · Cited by 526 · 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

An NMR Perspective on Enzyme Dynamics

Boehr, D. D., Dyson, H. J., & Wright, P. E. (2006) · Chemical Reviews · doi:10.1021/cr050312q · Cited by 460 · see citing works

Anisotropic network model: systematic evaluation and a new web interface

Eyal, E., Yang, L., & Bahar, İ. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl448 · Cited by 324 · see citing works

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

Bahar, I., Chennubhotla, C., & Tobi, D. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.09.011 · Cited by 306 · see citing works

Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

Chennubhotla, C., & Bahar, İ. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030172 · Cited by 230 · 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

A consensus view of protein dynamics

Rueda, M., Ferrer‐Costa, C., Meyer, T., Pérez, A., Camps, J., Gelpí, J. L., & Orozco, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605534104 · Cited by 225 · see citing works

Terahertz underdamped vibrational motion governs protein-ligand binding in solution

Turton, D. A., Senn, H. M., Harwood, T., Lapthorn, A. J., Ellis, E. M., & Wynne, K. (2014) · Nature Communications · doi:10.1038/ncomms4999 · Cited by 225 · see citing works

p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure–Function Continuum Concept

Uversky, V. N. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17111874 · Cited by 193 · see citing works

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

Chennubhotla, C., Rader, A. J., Yang, L., & Bahar, İ. (2005) · Physical Biology · doi:10.1088/1478-3975/2/4/s12 · Cited by 163 · see citing works

Sequence Evolution Correlates with Structural Dynamics

Liu, Y., & Bahar, İ. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss097 · Cited by 155 · see citing works

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

Rueda, M., Chacón, P., & Orozco, M. (2007) · Structure · doi:10.1016/j.str.2007.03.013 · Cited by 154 · see citing works

Protein intrinsic disorder and structure-function continuum

Uversky, V. N. (2019) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2019.05.003 · Cited by 155 · see citing works

Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

Chennubhotla, C., & Bahar, İ. (2006) · Molecular Systems Biology · doi:10.1038/msb4100075 · Cited by 151 · see citing works

o GNM: online computation of structural dynamics using the Gaussian Network Model

Yang, L., Rader, A. J., Liu, X., Jursa, C. J., Chen, S. C., Karimi, H. A., & Bahar, İ. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl084 · Cited by 145 · see citing works

DynOmics: dynamics of structural proteome and beyond

Li, H., Chang, Y.-Y., Lee, J. Y., Bahar, İ., & Yang, L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx385 · Cited by 137 · see citing works

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

Yang, L., Eyal, E., Bahar, İ., & Kitao, A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp023 · Cited by 135 · see citing works

Modulation of protein biophysical properties by chemical glycosylation: biochemical insights and biomedical implications

Solá, R. J., Rodríguez‐Martínez, J. A., & Griebenow, K. H. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-6551-y · Cited by 120 · see citing works

iGNM: a database of protein functional motions based on Gaussian Network Model

Yang, L.-W., Liu, X., Jursa, C. J., Holliman, M., Rader, A. J., Karimi, H. A., & Bahar, İ. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti469 · Cited by 119 · see citing works

Enzyme Inhibitors and Activators

Şentürk, M. (2017) · InTech eBooks · doi:10.5772/63325 · Cited by 113 · see citing works

NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps

Suhre, K., Navaza, J., & Sanejouand, Y. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744490602244x · Cited by 111 · see citing works

Normal Mode Analysis as a Routine Part of a Structural Investigation

Bauer, J., Pavlović, J., & Bauerová-Hlinková, V. (2019) · Molecules · doi:10.3390/molecules24183293 · Cited by 98 · see citing works

Enzymatic transition states and transition state analogues

Schramm, V. L. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.10.017 · Cited by 106 · see citing works

Structural dynamics flexibility informs function and evolution at a proteome scale

Gerek, Z. N., Kumar, S., & Ozkan, S. B. (2013) · Evolutionary Applications · doi:10.1111/eva.12052 · Cited by 104 · see citing works

Toward a quantitative theory of intrinsically disordered proteins and their function

Liu, J., Faeder, J. R., & Camacho, C. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907710106 · Cited by 102 · see citing works

Optimization and Evaluation of a Coarse-Grained Model of Protein Motion Using X-Ray Crystal Data

Kondrashov, D. A., Cui, Q., & Phillips, G. N. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.085894 · Cited by 103 · see citing works

Locating the active sites of enzymes using mechanical properties

Sacquin‐Mora, S., Laforet, É., & Lavery, R. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21353 · Cited by 97 · see citing works

Investigating the Local Flexibility of Functional Residues in Hemoproteins

Sacquin‐Mora, S., & Lavery, R. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.074997 · Cited by 93 · see citing works

Discrete Breathers in Nonlinear Network Models of Proteins

Juanico, B., Sanejouand, Y., Piazza, F., & Rios, P. D. L. (2007) · Physical Review Letters · doi:10.1103/physrevlett.99.238104 · Cited by 92 · see citing works

Time-resolved Mechanism of Extracellular Gate Opening and Substrate Binding in a Glutamate Transporter

Shrivastava, I. H., Jiang, J., Amara, S. G., & Bahar, İ. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800889200 · Cited by 91 · see citing works

Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines

Togashi, Y., & Mikhailov, A. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702950104 · Cited by 86 · see citing works

Binding Leverage as a Molecular Basis for Allosteric Regulation

Mitternacht, S., & Berezovsky, I. N. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002148 · Cited by 85 · see citing works

Interpreting Correlated Motions Using Normal Mode Analysis

Wynsberghe, A. W. V., & Cui, Q. (2006) · Structure · doi:10.1016/j.str.2006.09.003 · Cited by 81 · see citing works

On the relation between residue flexibility and local solvent accessibility in proteins

Zhang, H., Zhang, T., Chen, K., Shen, S., Ruan, J., & Kurgan, L. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22375 · Cited by 79 · see citing works

Deriving protein dynamical properties from weighted protein contact number

Lin, C., Huang, S., Lai, Y., Yen, S., Shih, C., Lu, C., Huang, C., & Hwang, J. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21983 · Cited by 78 · see citing works

Single-molecule Force Spectroscopy Approach to Enzyme Catalysis

Alegre‐Cebollada, J., Pérez‐Jiménez, R., Kosuri, P., & Fernández, J. M. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.r109.011932 · Cited by 78 · see citing works

Enhanced direct fermentation from food waste to butanol and hydrogen by an amylolytic Clostridium

Zhang, C., Li, T., Su, G., & He, J. (2020) · Renewable Energy · doi:10.1016/j.renene.2020.01.151 · Cited by 74 · see citing works

iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics

Li, H., Chang, Y.-Y., Yang, L., & Bahar, İ. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1236 · Cited by 73 · see citing works

Role of Hsp70 ATPase Domain Intrinsic Dynamics and Sequence Evolution in Enabling its Functional Interactions with NEFs

Liu, Y., Gierasch, L. M., & Bahar, İ. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000931 · Cited by 70 · see citing works

Enzyme Inhibitors and Activators

Lopina, O. D. (2017) · InTech eBooks · doi:10.5772/67248 · Cited by 70 · see citing works

Protein mechanics: a route from structure to function

Lavery, R., & Sacquin‐Mora, S. (2007) · Journal of Biosciences · doi:10.1007/s12038-007-0089-x · Cited by 69 · see citing works

Tenascin cytotactin epidermal growth factor‐like repeat binds epidermal growth factor receptor with low affinity

Iyer, A. K. V., Tran, K. T., Borysenko, C. W., Cascio, M., Camacho, C. J., Blair, H. C., Bahar, İ., & Wells, A. H. (2007) · Journal of Cellular Physiology · doi:10.1002/jcp.20986 · Cited by 69 · see citing works

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

Bahar, İ., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.004 · Cited by 67 · see citing works

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

Gerek, Z. N., Keskin, Ö., & Ozkan, S. B. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22492 · Cited by 66 · see citing works

Nucleotide-dependent Allostery within the ABC Transporter ATP-binding Cassette

Jones, P. M., & George, A. M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700809200 · Cited by 64 · see citing works

Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

Yang, L., & Chng, C. (2008) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s460 · Cited by 64 · see citing works

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

Tekpinar, M., & Zheng, W. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22755 · Cited by 62 · see citing works

Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

Zheng, W., & Tekpinar, M. (2009) · BMC Structural Biology · doi:10.1186/1472-6807-9-45 · Cited by 61 · see citing works

Long-range energy transfer in proteins

Piazza, F., & Sanejouand, Y.-H. (2009) · Physical Biology · doi:10.1088/1478-3975/6/4/046014 · Cited by 58 · see citing works

Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions

Ojeda-May, P., Mushtaq, A., Rogne, P., Verma, A., Ovchinnikov, V., Grundström, C., Dulko-Smith, B., Sauer, U., Wolf-Watz, M., & Nam, K. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00221 · Cited by 49 · see citing works

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Kurkcuoglu, Z., Bakan, A., Kocaman, D., Bahar, İ., & Doruker, P. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002705 · Cited by 58 · see citing works

On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

Bahar, İ. (2010) · The Journal of General Physiology · doi:10.1085/jgp.200910368 · Cited by 58 · see citing works

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Vishwanath, S., de Brevern, A. G., & Srinivasan, N. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006008 · Cited by 59 · see citing works

Crystal Structure of Helicobacter pylori Formamidase AmiF Reveals a Cysteine-Glutamate-Lysine Catalytic Triad

Hung, C.-L., Liu, J.-H., Chiu, W.-C., Huang, S., Hwang, J., & Wang, W. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m609134200 · Cited by 57 · see citing works

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation

Clarke, D., Sethi, A., Li, S., Kumar, S., Chang, R. W. F., Chen, J., & Gerstein, M. (2016) · Structure · doi:10.1016/j.str.2016.03.008 · Cited by 56 · see citing works

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Nam, K., Shao, Y., Major, D. T., & Wolf‐Watz, M. (2024) · ACS Omega · doi:10.1021/acsomega.3c09084 · Cited by 57 · see citing works

Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin–myosin light chain interaction

Delmotte, A., Tate, E. W., Yaliraki, S. N., & Barahona, M. (2011) · Physical Biology · doi:10.1088/1478-3975/8/5/055010 · Cited by 56 · see citing works

Interactions in Native Binding Sites Cause a Large Change in Protein Dynamics

Ming, D., & Wall, M. E. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.097 · Cited by 54 · see citing works

Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics

Dixit, A., & Verkhivker, G. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037605 · Cited by 53 · see citing works

Methods for Predicting Protein–Ligand Binding Sites

Xie, Z., & Hwang, M. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1465-4_17 · Cited by 53 · see citing works

Rigidity and flexibility of biological networks

Gaspar, M. E., & Csermely, P. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/els023 · Cited by 52 · see citing works

Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

Togashi, Y., & Flechsig, H. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19123899 · Cited by 51 · see citing works

Assessment of BAK1 activity in different plant receptor-like kinase complexes by quantitative profiling of phosphorylation patterns

Wang, Y., Li, Z., Liu, D., Xu, J., Wei, X., Yan, L., Yang, C., Lou, Z., & Shui, W. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.06.009 · Cited by 49 · see citing works

Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

Tse, A., & Verkhivker, G. M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166583 · Cited by 48 · see citing works

Thermodynamics of allostery paves a way to allosteric drugs

Berezovsky, I. N. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.01.024 · Cited by 47 · see citing works

Predisposition of the dark state of rhodopsin to functional changes in structure

Isin, B., Rader, A. J., Dhiman, H. K., Klein‐Seetharaman, J., & Bahar, İ. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21158 · Cited by 47 · see citing works

FlexOracle: predicting flexible hinges by identification of stable domains

Flores, S. C., & Gerstein, M. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-215 · Cited by 46 · see citing works

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics

Emperador, A., Carrillo, O., Rueda, M., & Orozco, M. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.119115 · Cited by 46 · see citing works

Protein Unfolding Behavior Studied by Elastic Network Model

Su, J. G., Li, C. H., Hao, R., Chen, W. Z., & Wang, C. X. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.121665 · Cited by 46 · see citing works

Analysis of correlated mutations in HIV-1 protease using spectral clustering

Liu, Y., Eyal, E., & Bahar, İ. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn110 · Cited by 45 · see citing works

Conformational flexibility ofMycobacterium tuberculosisthioredoxin reductase: crystal structure and normal-mode analysis

Akif, M., Suhre, K., Verma, C. S., & Mande, S. C. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905030519 · Cited by 44 · see citing works

Influence of modulated structural dynamics on the kinetics of α‐chymotrypsin catalysis

Solá, R. J., & Griebenow, K. H. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05524.x · Cited by 43 · see citing works

Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses

Szarecka, A., Xu, Y., & Tang, P. S. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.102780 · Cited by 43 · see citing works

HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors

Flores, S. C., Keating, K. S., Painter, J., Morcos, F., Nguyen, K., Merritt, E. A., Kuhn, L. A., & Gerstein, M. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22060 · Cited by 43 · see citing works

Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members

Mikulska‐Ruminska, K., Shrivastava, I. H., Krieger, J., Zhang, S., Li, H., Bayır, H., Wenzel, S. E., VanDemark, A. P., Kagan, V. E., & Bahar, İ. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00006 · Cited by 42 · see citing works

Isoflurane Alters the Structure and Dynamics of GLIC

Willenbring, D., Liu, L. T., Mowrey, D. D., Xu, Y., & Tang, P. S. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.09.026 · Cited by 42 · see citing works

Analysis of Domain Movements in Glutamine-Binding Protein with Simple Models

Su, J. G., Jiao, X., Sun, T. G., Li, C. H., Chen, W. Z., & Wang, C. X. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.086512 · Cited by 41 · see citing works

Dynamics of heteropentameric nicotinic acetylcholine receptor: Implications of the gating mechanism

Szarecka, A., Xu, Y., & Tang, P. S. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21462 · Cited by 41 · see citing works

On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm

Marcos, E., Crehuet, R., & Bahar, İ. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000738 · Cited by 40 · see citing works

The Application of 3D Zernike Moments for the Description of “Model-Free” Molecular Structure, Functional Motion, and Structural Reliability

Grandison, S., Roberts, C., & Morris, R. J. (2009) · Journal of Computational Biology · doi:10.1089/cmb.2008.0083 · Cited by 39 · see citing works

Allosteric Modulation of Intact γ-Secretase Structural Dynamics

Lee, J. Y., Feng, Z., Xie, X., & Bahar, İ. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.10.012 · Cited by 38 · see citing works

Catalytic activation of human glucokinase by substrate binding – residue contacts involved in the binding of D ‐glucose to the super‐open form and conformational transitions

Molnes, J., Bjørkhaug, L., Sövik, O., Njølstad, P. R., & Flatmark, T. (2008) · FEBS Journal · doi:10.1111/j.1742-4658.2008.06391.x · Cited by 38 · see citing works

Conservation of intrinsic dynamics in proteins — what have computational models taught us?

Tiwari, S. P., & Reuter, N. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.12.001 · Cited by 36 · see citing works

Fast dynamics perturbation analysis for prediction of protein functional sites

Ming, D., Cohn, J. D., & Wall, M. E. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-5 · Cited by 35 · see citing works

Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues

Yan, W., Hu, G., Liang, Z. T., Jianhong, Z., Yang, Y., Chen, J., & Shen, B. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00146 · Cited by 34 · see citing works

Structure–Stability–Activity Relationship in Covalently Cross-linked N-Carbamoyl d-Amino acid Amidohydrolase and N-Acylamino acid Racemase

Chiu, W.-C., You, J.-Y., Liu, J.-S., Hsu, S., Hsu, W.-H., Shih, C., Hwang, J., & Wang, W. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.03.063 · Cited by 33 · see citing works

Incorporating protein flexibility into docking and structure-based drug design

Barril, X., & Fradera, X. (2006) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.1.4.335 · Cited by 33 · see citing works

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods

Kaynak, B., Krieger, J., Dudás, B., Dahmani, Z. L., Costa, M. G. S., Balog, E., Scott, A. L., Doruker, P., Pérahia, D., & Bahar, İ. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.832847 · Cited by 32 · 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

Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

Sacquin‐Mora, S. (2015) · Journal of The Royal Society Interface · doi:10.1098/rsif.2015.0876 · Cited by 30 · see citing works

Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies

Macari, G., Toti, D., & Polticelli, F. (2019) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-019-00235-7 · Cited by 30 · see citing works

Metal-Binding Sites Are Designed to Achieve Optimal Mechanical and Signaling Properties

Dutta, A., & Bahar, İ. (2010) · Structure · doi:10.1016/j.str.2010.06.013 · Cited by 30 · see citing works

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 · see citing works

Rapid Catalytic Template Searching as an Enzyme Function Prediction Procedure

Nilmeier, J. P., Kirshner, D. A., Wong, S., & Lightstone, F. C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062535 · Cited by 28 · see citing works

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site

Streltsov, V. A., Luang, S., Peisley, A., Varghese, J. N., Cairns, J. R. K., Fort, S., Hijnen, M., Tvaroška, I., Ardá, A., Jiménez‐Barbero, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09691-z · Cited by 27 · see citing works

Universality of fold-encoded localized vibrations in enzymes

Chalopin, Y., Piazza, F., Mayboroda, S., Weisbuch, C., & Filoche, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-48905-8 · Cited by 27 · see citing works

Global dynamics behind enzyme catalysis, evolution, and design

Fas, B. A., Buz, Z. E. A., & Haliloǧlu, T. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103131 · Cited by 6 · see citing works

BIOMOLECULAR DYNAMICS REVEALED BY ELASTIC NETWORK MODELS AND THE STUDY OF MECHANICAL KEY SITES FOR LIGAND BINDING

Yang, L. (2005) · D-Scholarship@Pitt (University of Pittsburgh)

Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions

Ojeda-May, P., Mushtaq, A., Rogne, P., Verma, A., Ovchinnikov, V., Grundström, C., Dulko-Smith, B., Sauer, U., Wolf-Watz, M., & Nam, K. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00221 · Cited by 49 · see citing works

Computational Studies of Enzyme Motions

Cui, Q. (2012) · Springer eBooks · doi:10.1007/978-3-642-16712-6_161

Protein Motions Promote Catalysis

Tousignant, A., & Pelletier, J. N. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.06.007 · Cited by 116 · see citing works