Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations
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[1] M. Delarue,et al. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. , 2002, Journal of molecular biology.
[2] L Jen-Jacobson,et al. Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. , 1997, Biopolymers.
[3] H R Drew,et al. Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[4] D. Ming,et al. How to describe protein motion without amino acid sequence and atomic coordinates , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[5] Robert L. Jernigan,et al. Dynamics of large proteins through hierarchical levels of coarse‐grained structures , 2002, J. Comput. Chem..
[6] L. Nilsson,et al. Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation. , 1999, Biophysical journal.
[7] A. Atilgan,et al. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. , 1997, Folding & design.
[8] L. A. Jacobson,et al. Structural and thermodynamic strategies for site-specific DNA binding proteins. , 2000, Structure.
[9] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[10] W. Stec,et al. Mechanisms of coupling between DNA recognition specificity and catalysis in EcoRI endonuclease. , 2004, Structure.
[11] Jianpeng Ma,et al. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. , 2005, Structure.
[12] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[13] R. Jernigan,et al. Proteins with similar architecture exhibit similar large-scale dynamic behavior. , 2000, Biophysical journal.
[14] Robert L. Jernigan,et al. Collective Dynamics of Large Proteins from Mixed Coarse‐Grained Elastic Network Model , 2005 .
[15] Robert L Jernigan,et al. Loop motions of triosephosphate isomerase observed with elastic networks. , 2006, Biochemistry.
[16] B. Hess,et al. Similarities between principal components of protein dynamics and random diffusion , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[17] J M Rosenberg,et al. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. , 1990, Science.
[18] Ivet Bahar,et al. Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. , 2002, Biophysical journal.
[19] S Sen,et al. Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex. , 1999, Biophysical journal.
[20] R L Jernigan,et al. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. , 1998, Journal of molecular biology.
[21] A. Atilgan,et al. Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability , 1998 .
[22] J M Rosenberg,et al. Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases. , 1996, Journal of molecular biology.
[23] Ivet Bahar,et al. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor , 2000, Proteins.
[24] H. Berendsen,et al. Essential dynamics of proteins , 1993, Proteins.
[25] J. Rosenberg. Structure and function of restriction endonucleases , 1991 .
[26] H. Berendsen,et al. Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme , 1998, Proteins.
[27] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[28] R. Jernigan,et al. Global ribosome motions revealed with elastic network model. , 2004, Journal of structural biology.
[29] H. Berendsen,et al. Model‐free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme , 1997, Proteins.
[30] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[31] M. Levitt,et al. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. , 1985, Journal of molecular biology.
[32] M. Karplus,et al. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin , 1998, Protein science : a publication of the Protein Society.
[33] A. Jeltsch,et al. Structure and function of type II restriction endonucleases. , 2001, Nucleic acids research.
[34] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[35] Ricardo L Mancera,et al. Comparative estimation of vibrational entropy changes in proteins through normal modes analysis. , 2004, Journal of molecular graphics & modelling.
[36] P. Kollman,et al. Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. , 1994, Journal of biomolecular structure & dynamics.
[37] A. Elofsson,et al. How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin. , 1993, Journal of molecular biology.
[38] Burak Alakent,et al. Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis. , 2004, The Journal of chemical physics.
[39] Robert L Jernigan,et al. Functional motions can be extracted from on‐lattice construction of protein structures , 2003, Proteins.
[40] Bhyravabhotla Jayaram,et al. Free Energy Analysis of Protein-DNA Binding , 1999 .
[41] Robert L. Jernigan,et al. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions , 2004 .
[42] W. Wriggers,et al. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. , 2002, Journal of molecular biology.
[43] P. Doruker,et al. Collective Motions of RNA Polymerases. Analysis of Core Enzyme, Elongation Complex and Holoenzyme , 2004, Journal of biomolecular structure & dynamics.
[44] R. Nussinov,et al. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. , 2005, Biophysical journal.
[45] A. Maritan,et al. Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models , 2004, Proteins.