Advances in coarse-grained modeling of macromolecular complexes.

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[31]  Guang Song,et al.  Generalized spring tensor models for protein fluctuation dynamics and conformation changes. , 2014, Advances in experimental medicine and biology.

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[37]  Alexey Savelyev,et al.  Chemically accurate coarse graining of double-stranded DNA , 2010, Proceedings of the National Academy of Sciences.

[38]  Ivet Bahar,et al.  Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model , 2014, PLoS Comput. Biol..

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[41]  Gregory A Voth,et al.  Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. , 2018, Biophysical journal.

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[44]  Gregory A Voth,et al.  Coarse-graining of multiprotein assemblies. , 2012, Current opinion in structural biology.

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[57]  J. Williamson,et al.  Cooperativity in macromolecular assembly. , 2008, Nature chemical biology.

[58]  Fangqiang Zhu,et al.  Mechanism of polymorphism and curvature of HIV capsid assemblies probed by 3D simulations with a novel coarse grain model. , 2015, Biochimica et biophysica acta.

[59]  F. Huber,et al.  Emergent complexity of the cytoskeleton: from single filaments to tissue , 2013, Advances in physics.

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[63]  Gregory A Voth,et al.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. , 2008, The Journal of chemical physics.

[64]  Kyle M. Douglass,et al.  Super-resolution microscopy to decipher multi-molecular assemblies. , 2018, Current opinion in structural biology.

[65]  Patrice Koehl,et al.  The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems. , 2017, Journal of chemical theory and computation.

[66]  P. Doruker,et al.  RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network Model. , 2018, The journal of physical chemistry. B.

[67]  Changbong Hyeon,et al.  Dynamics of allosteric transitions in GroEL , 2006, Proceedings of the National Academy of Sciences.

[68]  F. Major,et al.  The Elastic Network Contact Model applied to RNA: enhanced accuracy for conformational space prediction , 2017, bioRxiv.

[69]  D. Thirumalai,et al.  Kinematics of the lever arm swing in myosin VI , 2016, Proceedings of the National Academy of Sciences.

[70]  Gregory A Voth,et al.  Coarse-Grained Directed Simulation. , 2017, Journal of chemical theory and computation.

[71]  Michael R DeLyser,et al.  Extending pressure-matching to inhomogeneous systems via local-density potentials. , 2017, The Journal of chemical physics.

[72]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[73]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.

[74]  Oliver Brock,et al.  Elastic network model of learned maintained contacts to predict protein motion , 2017, PloS one.

[75]  Cecilia Clementi,et al.  Learning Effective Molecular Models from Experimental Observables. , 2018, Journal of chemical theory and computation.

[76]  S. Melchionna,et al.  Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. , 2015, Journal of chemical theory and computation.

[77]  J. Woolford,et al.  Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo. , 2015, Annual review of biochemistry.

[78]  Antony K. Chen,et al.  Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane , 2017, Proceedings of the National Academy of Sciences.

[79]  Joseph F. Rudzinski,et al.  Bottom-Up Coarse-Graining of Peptide Ensembles and Helix-Coil Transitions. , 2015, Journal of chemical theory and computation.

[80]  G. Voth,et al.  Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. , 2018, Journal of chemical theory and computation.

[81]  J. Onuchic,et al.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.

[82]  Fei Xia,et al.  Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization. , 2016, Journal of chemical theory and computation.

[83]  Robert B Best,et al.  Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model. , 2014, The Journal of chemical physics.

[84]  L. M. Mansky,et al.  Morphology and ultrastructure of retrovirus particles , 2015, AIMS biophysics.

[85]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.

[86]  Ian R Kleckner,et al.  An introduction to NMR-based approaches for measuring protein dynamics. , 2011, Biochimica et biophysica acta.

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[89]  M. Wolf-Watz,et al.  Protein dynamics and function from solution state NMR spectroscopy , 2016, Quarterly Reviews of Biophysics.

[90]  M Scott Shell,et al.  A new multiscale algorithm and its application to coarse-grained peptide models for self-assembly. , 2012, The journal of physical chemistry. B.

[91]  Sungsoo Na,et al.  Mechanical Characterization of Amyloid Fibrils Using Coarse‐Grained Normal Mode Analysis , 2011, 1105.1788.

[92]  Kurt Kremer,et al.  A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site , 2016, Proteins.

[93]  R. Jernigan,et al.  Knowledge-based entropies improve the identification of native protein structures , 2017, Proceedings of the National Academy of Sciences.

[94]  M. Shell,et al.  Transferable Coarse-Grained Models of Liquid-Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy. , 2018, The journal of physical chemistry. B.

[95]  Jeremy C. Smith,et al.  REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. , 2009, Biophysical journal.

[96]  Gregory A Voth,et al.  Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data. , 2010, Journal of chemical theory and computation.

[97]  R. Dima,et al.  Molecular investigations into the mechanics of actin in different nucleotide states. , 2011, The journal of physical chemistry. B.

[98]  Michael Habeck,et al.  Data-driven coarse graining of large biomolecular structures , 2017, PloS one.

[99]  J A McCammon,et al.  Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems. , 2006, Journal of chemical theory and computation.

[100]  Aleksander E. P. Durumeric,et al.  On the representability problem and the physical meaning of coarse-grained models. , 2016, The Journal of chemical physics.

[101]  Rafael Najmanovich,et al.  A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations , 2013, bioRxiv.

[102]  M Scott Shell,et al.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.