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

Efficient Generation of Feasible Pathways for Protein Conformational Transitions

Kim, M. K., Jernigan, R. L., & Chirikjian, G. S. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)73931-3 · Cited by 173

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

Best, R. B., Chen, Y.-G., & Hummer, G. (2005) · Structure · doi:10.1016/j.str.2005.08.009 · Cited by 173

Convergence of molecular dynamics simulations of membrane proteins

Grossfield, A., Feller, S. E., & Pitman, M. C. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21308 · Cited by 172

Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

Yang, L., Song, G., Carriquiry, A., & Jernigan, R. L. (2008) · Structure · doi:10.1016/j.str.2007.12.011 · Cited by 171

Molecular Dynamics Study of the KcsA Potassium Channel

Allen, T. W., Kuyucak, S., & Chung, S.-H. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)77086-4 · Cited by 169

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

Lyman, E., Pfaendtner, J., & Voth, G. A. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.139733 · Cited by 168

Molecular Dynamics Investigation of Primary Photoinduced Eventsin the Activation of Rhodopsin

Saam, J., Tajkhorshid, E., Hayashi, S., & Schulten, K. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75314-9 · Cited by 168

A new approach for determining low‐frequency normal modes in macromolecules

Durand, P., Trinquier, G., & Sanejouand, Y. (1994) · Biopolymers · doi:10.1002/bip.360340608 · Cited by 167

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

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

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

Bahar, I., Wallqvist, A., Covell, D. G., & Jernigan, R. L. (1998) · Biochemistry · doi:10.1021/bi9720641 · Cited by 167

Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening

Cavasotto, C. N., Orry, A. J. W., Murgolo, N. J., Czarniecki, M. F., Kocsi, S. A., Hawes, B. E., O’Neill, K. A., Hine, H., Burton, M. S., Voigt, J. H., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm070759m · Cited by 167

Identification of core amino acids stabilizing rhodopsin

Rader, A. J., Anderson, G., Isin, B., Khorana, H. G., Bahar, I., & Klein-Seetharaman, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401429101 · Cited by 166

Allostery in a Coarse-Grained Model of Protein Dynamics

Ming, D., & Wall, M. E. (2005) · Physical Review Letters · doi:10.1103/physrevlett.95.198103 · Cited by 165

The Membrane Protein Data Bank

Raman, P., Cherezov, V., & Caffrey, M. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-5350-6 · Cited by 164

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

Chennubhotla, C., Rader, A. J., Yang, L.-W., & Bahar, I. (2005) · Physical Biology · doi:10.1088/1478-3975/2/4/s12 · Cited by 162

Probing ion-channel pores one proton at a time

Cymes, G. D., Ni, Y., & Grosman, C. (2005) · Nature · doi:10.1038/nature04293 · Cited by 159

Time-Resolved Detection of Structural Changes During the Photocycle of Spin-Labeled Bacteriorhodopsin

Steinhoff, H., Mollaaghababa, R., Altenbach, C., Hideg, K., Krebs, M. P., Khorana, H. G., & Hubbell, W. L. (1994) · Science · doi:10.1126/science.7939627 · Cited by 155

High-resolution Structures of the Ligand Binding Domain of the Wild-type Bacterial Aspartate Receptor

Yeh, J. I., Biemann, H.-P., Privé, G. G., Pandit, J., Koshland, D. E., & Kim, S. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0507 · Cited by 153

Structural Features of the Glutamate Transporter Family

Slotboom, D. J., Konings, W. N., & Lolkema, J. S. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.293-307.1999 · Cited by 151

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

Effects of ion binding on the backbone dynamics of calbindin D9k determined by nitrogen-15 NMR relaxation

Akke, M., Skelton, N. J., Kördel, J., Palmer, A. G. I., & Chazin, W. (1993) · Biochemistry · doi:10.1021/bi00088a039 · Cited by 150

Glutamate and monoamine transporters: new visions of form and function

Torres, G. E., & Amara, S. (2007) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2007.05.002 · Cited by 147

G protein-coupled receptors: In silico drug discovery in 3D

Becker, O. M., Marantz, Y., Shacham, S., Inbal, B., Heifetz, A., Kalid, O., Bar‐Haim, S., Warshaviak, D. T., Fichman, M., & Noiman, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401862101 · Cited by 147

How do membrane proteins sense water stress?

Poolman, B., Blount, P., Folgering, J. H. A., Friesen, R. H. E., Moe, P. C., & van der Heide, T. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02894.x · Cited by 146

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

Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular Force Fields

Allen, T. W., Andersen, O. S., & Roux, B. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.077073 · Cited by 144

Membrane Model for the G-Protein-Coupled Receptor Rhodopsin: Hydrophobic Interface and Dynamical Structure

Huber, T., Botelho, A. V., Beyer, K., & Brown, M. F. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74268-x · Cited by 144

K+ versus Na+ Ions in a K Channel Selectivity Filter: A Simulation Study

Shrivastava, I. H., Tieleman, D. P., Biggin, P. C., & Sansom, M. S. P. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75197-7 · Cited by 144

Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions

Yang, L., Eyal, E., Chennubhotla, C., Jee, J., Gronenborn, A. M., & Bahar, İ. (2007) · Structure · doi:10.1016/j.str.2007.04.014 · Cited by 138

A stepwise mechanism for acetylcholine receptor channel gating

Purohit, P. G., Mitra, A., & Auerbach, A. L. (2007) · Nature · doi:10.1038/nature05721 · Cited by 137

Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model

Chu, J., & Voth, G. A. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.112060 · Cited by 136

The Role of Shape in Determining Molecular Motions

Lu, M., & Ma, J. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.065904 · Cited by 136

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL

Yang, Z., Májek, P., & Bahar, İ. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000360 · Cited by 136

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

Computational Studies of the Gramicidin Channel

Roux, B. (2002) · Accounts of Chemical Research · doi:10.1021/ar010028v · Cited by 134

Collective protein dynamics and nuclear spin relaxation

Brüschweiler, R. (1995) · The Journal of Chemical Physics · doi:10.1063/1.469213 · Cited by 132

Molecular Modeling of the Three-Dimensional Structure of Dopamine 3 (D3) Subtype Receptor: Discovery of Novel and Potent D3Ligands through a Hybrid Pharmacophore- and Structure-Based Database Searching Approach

Varady, J., Wu, X., Fang, X., Ji, M., Hu, Z., Levant, B., & Wang, S. (2003) · Journal of Medicinal Chemistry · doi:10.1021/jm030085p · Cited by 131

Membrane protein structure: experimental approaches

White, S. H. (1994) · Oxford University Press eBooks · Cited by 126

How lipids and proteins interact in a membrane: a molecular approach

LEE, A. G. J. (2005) · Molecular BioSystems · doi:10.1039/b504527d · Cited by 125

Probing Side-Chain Dynamics in the Proteasome by Relaxation Violated Coherence Transfer NMR Spectroscopy

Tugarinov, V., Sprangers, R., & Kay, L. E. (2007) · Journal of the American Chemical Society · doi:10.1021/ja067827z · Cited by 123

Formation of the meta II photointermediate is accompanied by conformational changes in the cytoplasmic surface of rhodopsin

Resek, J. F., Farahbakhsh, Z. T., Hubbell, W. L., & Khorana, H. G. (1993) · Biochemistry · doi:10.1021/bi00096a012 · Cited by 119

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

Structural flexibility in proteins: impact of the crystal environment

Hinsen, K. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm625 · Cited by 119

Global Twisting Motion of Single Molecular KcsA Potassium Channel upon Gating

Shimizu, H., Iwamoto, M., Konno, T., Nihei, A., Sasaki, Y. C., & Oiki, S. (2008) · Cell · doi:10.1016/j.cell.2007.11.040 · Cited by 118

Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics

Lakomek, N., Walter, K. F. A., Farès, C., Lange, O. F., de Groot, B. L., Grubmüller, H., Brüschweiler, R., Munk, A., Becker, S., Meiler, J., et al. (2008) · Journal of Biomolecular NMR · doi:10.1007/s10858-008-9244-4 · Cited by 116

Langevin modes of macromolecules

Lamm, G., & Szabó, A. (1986) · The Journal of Chemical Physics · doi:10.1063/1.451373 · Cited by 115

SPIN LABELED CYSTEINES AS SENSORS FOR PROTEIN‐LIPID INTERACTION AND CONFORMATION IN RHODOPSIN

Farahbakhsh, Z. T., Altenbach, C., & Hubbell, W. L. (1992) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.1992.tb09725.x · Cited by 113

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

Channel Opening Motion of α7 Nicotinic Acetylcholine Receptor as Suggested by Normal Mode Analysis

Cheng, X., Lu, B., Grant, B. J., et al. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.10.039 · Cited by 109

Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields

Allen, T. W., Baştuğ, T., Kuyucak, S., et al. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)75022-x · Cited by 108

Accounting for global protein deformability during protein–protein and protein–ligand docking

May, A., & Zacharias, M. (2005) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2005.07.045 · Cited by 107

Simulation of Domain Formation in DLPC−DSPC Mixed Bilayers

Faller, R., & Marrink, ‪. J. (2004) · Langmuir · doi:10.1021/la0492759 · Cited by 107

PREDICT modeling and in‐silico screening for G‐protein coupled receptors

Shacham, S., Marantz, Y., Bar‐Haim, S., Kalid, O., Warshaviak, D. T., Avisar, N., Inbal, B., Heifetz, A., Fichman, M., Topf, M., et al. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20195 · Cited by 106

Motions in Hemoglobin Studied by Normal Mode Analysis and Energy Minimization: Evidence for the Existence of Tertiary T-like, Quaternary R-like Intermediate Structures

Mouawad, L., & Perahia, D. G. S. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0257 · Cited by 103

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

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

Chennubhotla, C., Yang, Z., & Bahar, I. (2008) · Molecular BioSystems · doi:10.1039/b717819k · Cited by 102

Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in Distance between Residue 316 in Helix 8 and Residues in the Sequence 60−75, Covering the Cytoplasmic End of Helices TM1 and TM2 and Their Connection Loop CL1

Altenbach, C., Klein‐Seetharaman, J., Cai, K., Khorana, H. G., & Hubbell, W. L. (2001) · Biochemistry · doi:10.1021/bi011545o · Cited by 102

Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data

Haliloǧlu, T., & Bahar, İ. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19991201)37:4<654::aid-prot15>3.0.co;2-j · Cited by 101

Infrared Analysis of the Structure of Amino Acids, Polypeptides and Proteins

Sutherland, G. B. B. M. (1952) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60021-2 · Cited by 98

Maturation Dynamics of Bacteriophage HK97 Capsid

Rader, A. J., Vlad, D. H., & Bahar, İ. (2005) · Structure · doi:10.1016/j.str.2004.12.015 · Cited by 98

Early Steps of the Intramolecular Signal Transduction in Rhodopsin Explored by Molecular Dynamics Simulations

Röhrig, U. F., Guidoni, L., & Röthlisberger, U. (2002) · Biochemistry · doi:10.1021/bi026011h · Cited by 98

Functional Modes of Proteins Are among the Most Robust

Nicolay, S., & Sanejouand, Y. (2006) · Physical Review Letters · doi:10.1103/physrevlett.96.078104 · Cited by 96

A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase

Vėlyvis, A., Yang, Y. R., Schachman, H. K., & Kay, L. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703347104 · Cited by 96

Probing the Local Dynamics of Nucleotide-Binding Pocket Coupled to the Global Dynamics: Myosin versus Kinesin

Zheng, W., & Brooks, B. R. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.063305 · Cited by 96

Lipid−Protein Interactions Studied by Introduction of a Tryptophan Residue: The Mechanosensitive Channel MscL

Powl, A. M., East, J. M., & LEE, A. G. J. (2003) · Biochemistry · doi:10.1021/bi034995k · Cited by 96

Implications of the quaternary twist allosteric model for the physiology and pathology of nicotinic acetylcholine receptors

Taly, A., Corringer, P., Grütter, T., de Carvalho, L. P., Karplus, M., & Changeux, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607477103 · Cited by 95

Structure and Function in Rhodopsin: Mapping Light-Dependent Changes in Distance between Residue 65 in Helix TM1 and Residues in the Sequence 306−319 at the Cytoplasmic End of Helix TM7 and in Helix H8

Altenbach, C., Cai, K., Klein‐Seetharaman, J., Khorana, H. G., & Hubbell, W. L. (2001) · Biochemistry · doi:10.1021/bi011546g · Cited by 94

Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian

Moritsugu, K., & Smith, J. C. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.111898 · Cited by 93

Molecular Dynamics Simulation of Dark-adapted Rhodopsin in an Explicit Membrane Bilayer: Coupling between Local Retinal and Larger Scale Conformational Change

Crozier, P., Stevens, M. J., Forrest, L. R., & Woolf, T. B. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.08.045 · Cited by 92

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

Quantifying allosteric effects in proteins

Ming, D., & Wall, M. E. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20440 · Cited by 91

Common Mechanism of Pore Opening Shared by Five Different Potassium Channels

Shrivastava, I. H., & Bahar, İ. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.080093 · Cited by 91

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

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

Two‐dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins

Stahlberg, H., Fotiadis, D., Simon Scheuring, A., Remigy, H., Braun, T., Mitsuoka, K., Fujiyoshi, Y., & Engel, A. H. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02746-6 · Cited by 90

Experimental Verification of Conformational Variation of Human Fatty Acid Synthase as Predicted by Normal Mode Analysis

Brink, J., Ludtke, S. J., Kong, Y., Wakil, S. J., Ma, J., & Chiu, W. (2004) · Structure · doi:10.1016/j.str.2004.01.015 · Cited by 90

Structural analysis of ion selectivity in the NaK channel

Alam, A., & Jiang, Y. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1537 · Cited by 89

Conformational Transitions Induced by the Binding of MgATP to the Vitamin B12 ATP-binding Cassette (ABC) Transporter BtuCD

Oloo, E. O., & Tieleman, D. P. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m405084200 · Cited by 89

Normal Mode-Based Fitting of Atomic Structure into Electron Density Maps: Application to Sarcoplasmic Reticulum Ca-ATPase

Hinsen, K., Reuter, N., Navaza, J., Stokes, D. L., & Lacapère, J.-J. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.050716 · Cited by 89

Conformational States and Dynamics of Rhodopsin in Micelles and Bilayers

Kusnetzow, A. K., Altenbach, C., & Hubbell, W. L. (2006) · Biochemistry · doi:10.1021/bi060101v · Cited by 89

Single-molecule spectroscopy of the β 2 adrenergic receptor: Observation of conformational substates in a membrane protein

Peleg, G., Ghanouni, P., Kobilka, B. K., & Zare, R. N. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.151239698 · Cited by 88

Normal-Modes-Based Prediction of Protein Conformational Changes Guided by Distance Constraints

Zheng, W., & Brooks, B. R. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.058453 · Cited by 88

MATLAB for Engineers

Moore, H. J. (2006) · Cited by 87

Analysis of Functional Motions in Brownian Molecular Machines with an Efficient Block Normal Mode Approach: Myosin-II and Ca2+-ATPase

Li, G., & Cui, Q. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74152-1 · Cited by 87

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

May, A., & Zacharias, M. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800071v · Cited by 83

Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies

Kim, M., Jernigan, R. L., & Chirikjian, G. S. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.044347 · Cited by 82

Gain-of-function Mutations Reveal Expanded Intermediate States and a Sequential Action of Two Gates in MscL

Anishkin, A., Chiang, C.-S., & Sukharev, S. (2005) · The Journal of General Physiology · doi:10.1085/jgp.200409118 · Cited by 82

Efficient Characterization of Collective Motions and Interresidue Correlations in Proteins by Low-Resolution Simulations

Bahar, İ., Erman, B., Haliloǧlu, T., & Jernigan, R. L. (1997) · Biochemistry · doi:10.1021/bi971611f · Cited by 79

An elastic network model of HK97 capsid maturation

Kim, M., Jernigan, R. L., & Chirikjian, G. S. (2003) · Journal of Structural Biology · doi:10.1016/s1047-8477(03)00126-6 · Cited by 78

Automatic identification of discrete substates in proteins: Singular value decomposition analysis of time‐averaged crystallographic refinements

Romo, T. D., Clarage, J. B., Sorensen, D. C., & Phillips, G. N. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340220403 · Cited by 78

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models

Eyal, E., Chennubhotla, C., Yang, L., & Bahar, İ. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm186 · Cited by 78

Structure‐based identification of binding sites, native ligands and potential inhibitors for G‐protein coupled receptors

Cavasotto, C. N., Orry, A. J. W., & Abagyan, R. A. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10362 · Cited by 76

Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes

Isin, B., Schulten, K. J., Tajkhorshid, E., & Bahar, İ. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.120691 · Cited by 76

Quantitative 13C and 2H NMR Relaxation Studies of the 723-Residue Enzyme Malate Synthase G Reveal a Dynamic Binding Interface

Tugarinov, V., & Kay, L. E. (2005) · Biochemistry · doi:10.1021/bi0519809 · Cited by 74

Structure and Dynamics of Pin1 During Catalysis by NMR

Labeikovsky, W., Eisenmesser, E. Z., Bosco, D. A., & Kern, D. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.049 · Cited by 74

Scattered Intensity from a Chain in a Rubber Network

Pearson, D. S. (1977) · Macromolecules · doi:10.1021/ma60057a040 · Cited by 73

An enhanced elastic network model to represent the motions of domain‐swapped proteins

Song, G., & Jernigan, R. L. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20836 · Cited by 72

Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family

Maguid, S., Fernández-Alberti, S., Ferrelli, M. L., & Echave, J. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.053041 · Cited by 72

vGNM: A Better Model for Understanding the Dynamics of Proteins in Crystals

Song, G., & Jernigan, R. L. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.03.059 · Cited by 72

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

Floquet, N., Maréchal, J., Badet‐Denisot, M., Robert, C. H., Dauchez, M., & Pérahia, D. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.08.037 · Cited by 67

Inherent Dynamics of the Acid-Sensing Ion Channel 1 Correlates with the Gating Mechanism

Yang, H., Yu, Y., Li, W., Yu, F., Cao, H., Xu, T., & Jiang, H. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000151 · Cited by 67

Folding core predictions from network models of proteins

Rader, A. J., & Bahar, İ. (2003) · Polymer · doi:10.1016/j.polymer.2003.10.080 · Cited by 67

Coupling of Global and Local Vibrational Modes in Dynamic Allostery of Proteins

Hawkins, R. J., & McLeish, T. C. B. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.082180 · Cited by 63

ABC transporter architecture and mechanism: implications from the crystal structures of BtuCD and BtuF

Locher, K. P., & Borths, E. L. (2004) · FEBS Letters · doi:10.1016/s0014-5793(04)00289-3 · Cited by 62

Normal-Mode Flexible Fitting of High-Resolution Structure of Biological Molecules toward One-Dimensional Low-Resolution Data

Gorba, C., Miyashita, O., & Tama, F. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.122218 · Cited by 61

Normal mode analysis

Field, M. J. (2007) · Cambridge University Press eBooks · doi:10.1017/cbo9780511619076.010 · Cited by 58

Protein dynamics simulations from nanoseconds to microseconds

Doniach, S., & Eastman, P. K. (1999) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(99)80022-0 · Cited by 58

The Dynamics of the MgATP-driven Closure of MalK, the Energy-transducing Subunit of the Maltose ABC Transporter

Oloo, E. O., Fung, E. Y., & Tieleman, D. P. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m513614200 · Cited by 58

COMPUTER SIMULATIONS OF TRANSPORT THROUGH MEMBRANES: PASSIVE DIFFUSION, PORES, CHANNELS AND TRANSPORTERS

Tieleman, D. P. (2006) · Clinical and Experimental Pharmacology and Physiology · doi:10.1111/j.1440-1681.2006.04461.x · Cited by 58

Photoisomerization Mechanism of Rhodopsin and 9-cis-Rhodopsin Revealed by X-ray Crystallography

Nakamichi, H., Buß, V., & Okada, T. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.108225 · Cited by 58

Functional Dynamics of Human FKBP12 Revealed by Methyl 13 C Rotating Frame Relaxation Dispersion NMR Spectroscopy

Brath, U., Akke, M., Yang, D., Kay, L. E., & Mulder, F. A. A. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0570279 · Cited by 57

Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation

Garcı́a, A. E., & Harman, J. G. (1996) · Protein Science · doi:10.1002/pro.5560050108 · Cited by 55

Identification of the Hydrophobic Thickness of a Membrane Protein Using Fluorescence Spectroscopy: Studies with the Mechanosensitive Channel MscL,1

Powl, A. M., Wright, J. N., East, J. M., et al. (2005) · Biochemistry · doi:10.1021/bi047338g · Cited by 54

Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks

Kürkçüoğlu, Ö., Jernigan, R. L., & Doruker, P. (2005) · Biochemistry · doi:10.1021/bi0518085 · Cited by 54

Alternative models for two crystal structures of bovine rhodopsin

Stenkamp, R. E. (2008) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444908017162 · Cited by 54

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 52

Propagation of Dynamic Changes in Barnase Upon Binding of Barstar: An NMR and Computational Study

Zhuravleva, A., Korzhnev, D. M., Nolde, S. B., Kay, L. E., Arseniev, A. S., Billeter, M., & Orekhov, V. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.01.051 · Cited by 52

Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer

Cymes, G. D., & Grosman, C. F. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1407 · Cited by 51

Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor

Liu, X., Xu, Y., Li, H., Wang, X., Jiang, H., & Barrantes, F. J. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040019 · Cited by 51

In SilicoModels for the Human α4β2 Nicotinic Acetylcholine Receptor

Haddadian, E. J., Cheng, M. H., Coalson, R. D., Xu, Y., & Tang, P. S. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp804868s · Cited by 49

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 47

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

NMR studies of a channel protein without membranes: Structure and dynamics of water-solubilized KcsA

Ma, D., Tillman, T. S., Tang, P. S., Meirovitch, E., Eckenhoff, R. G., Carnini, A., & Xu, Y. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805501105 · Cited by 46

Conformational Dynamics of the Ligand-Binding Domain of Inward Rectifier K Channels as Revealed by Molecular Dynamics Simulations: Toward an Understanding of Kir Channel Gating

Haider, S. M., Grottesi, A., Hall, B. A., Ashcroft, F. M., & Sansom, M. S. P. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.052019 · Cited by 45

Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems

Hamacher, K., & McCammon, J. A. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct050247s · Cited by 45

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

Sampling of near‐native protein conformations during protein structure refinement using a coarse‐grained model, normal modes, and molecular dynamics simulations

Stumpff‐Kane, A. W., Maksimiak, K., Lee, M. S., & Feig, M. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21674 · Cited by 41

Molecular Dynamics Simulations of Retinal in Rhodopsin: From the Dark-Adapted State towards Lumirhodopsin

Lemaître, V., Yèagle, P. L., & Watts, A. G. (2005) · Biochemistry · doi:10.1021/bi0506019 · Cited by 41

The dual-function glutamate transporters: structure and molecular characterisation of the substrate-binding sites

Kanner, B. I., & Borre, L. (2002) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(02)00260-8 · Cited by 40

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

Lu, M., & Ma, J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806072105 · Cited by 39

Vibrational Dynamics of Icosahedrally Symmetric Biomolecular Assemblies Compared with Predictions Based on Continuum Elasticity

Yang, Z., Bahar, İ., & Widom, M. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2009.03.016 · Cited by 39

A Comparison Between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA

Kim, M., Li, W., Shapiro, B. A., & Chirikjian, G. S. (2003) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2003.10506935 · Cited by 34

Conformational heterogeneity and low-frequency vibrational modes of proteins

Balog, E., Smith, J. C., & Pérahia, D. (2006) · Physical Chemistry Chemical Physics · doi:10.1039/b610075a · Cited by 28

The Conformational Coupling and Translocation Mechanism of Vitamin B12 ATP-Binding Cassette Transporter BtuCD

Weng, J., Ma, J., Fan, K., & Wang, W. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.110734 · Cited by 22

Cooperative Transition between Open and Closed Conformations in Potassium Channels

Haliloǧlu, T., & Ben‐Tal, N. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000164 · Cited by 22

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X‐ray, and computations

Liu, L., Koharudin, L. M. I., Gronenborn, A. M., & Bahar, İ. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22518 · Cited by 20

Langevin Network Model of Myosin

Miller, B. T., Zheng, W., Venable, R. M., Pastor, R. W., & Brooks, B. R. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp077042v · Cited by 17

Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1

Maréchal, J., & Perahia, D. G. S. (2008) · European Biophysics Journal · doi:10.1007/s00249-008-0279-y · Cited by 11

What determines the spectrum of protein native state structures?

Lezon, T. R., Banavar, J. R., Lesk, A. M., & Maritan, A. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20869 · Cited by 8

Loop entanglement of semicrystalline polyethylene in amorphous region: Diamond lattice approach

Duan, Z.-H., & Howard, L. N. (1999) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199902)20:3<287::aid-jcc1>3.0.co;2-h · Cited by 4

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky300 · Cited by 1,086

Perspective: Coarse-grained models for biomolecular systems

Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893

GPCR Dynamics: Structures in Motion

Latorraca, N. R., Venkatakrishnan, A. J., & Dror, R. O. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00177 · Cited by 835

Global dynamics of proteins: bridging between structure and function

Bahar, I., Lezon, T. R., Yang, L.-W., & Eyal, E. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.093008.131258 · Cited by 610

An introduction to NMR-based approaches for measuring protein dynamics

Kleckner, I. R., & Foster, M. P. (2011) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2010.10.012 · Cited by 561