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PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
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BIOINFORMATICS (2009)
Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits
R. Potestio et al.
BIOPHYSICAL JOURNAL (2009)
Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models
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BIOPHYSICAL JOURNAL (2009)
Insights from Coarse-Grained Go Models for Protein Folding and Dynamics
Ronald D. Hills et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2009)
Multiscale network model for large protein dynamics
Hyoseon Jang et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Extended ensemble approach for deriving transferable coarse-grained potentials
J. W. Mullinax et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Coupling atomistic and continuum hydrodynamics through a mesoscopic model: Application to liquid water
Rafael Delgado-Buscalioni et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Generic coarse-grained model for protein folding and aggregation
Tristan Bereau et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Invariant Polymorphism in Virus Capsid Assembly
Hung D. Nguyen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
Paul C. Whitford et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Discovery Through the Computational Microscope
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STRUCTURE (2009)
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Peter L. Freddolino et al.
BIOPHYSICAL JOURNAL (2008)
A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules
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Anton, a special-purpose machine for molecular dynamics simulation
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COMMUNICATIONS OF THE ACM (2008)
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A novel algorithm for creating coarse-grained, density dependent implicit solvent models
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Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
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The relative entropy is fundamental to multiscale and inverse thermodynamic problems
M. Scott Shell
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The MARTINI coarse-grained force field: Extension to proteins
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Knowledge-based potential for the polypeptide backbone
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Single molecule conformational dynamics of adenylate kinase: Energy landscape, structural correlations, and transition state ensembles
Qiang Lu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
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PHYSICAL REVIEW LETTERS (2008)
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JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
A coarse-grained protein force field for folding and structure prediction
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Network analysis of protein dynamics
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FEBS LETTERS (2007)
Coarse-graining of protein structures for the normal mode studies
Kilho Eom et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Dynamics of allosteric transitions in GroEL
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
Anton Arkhipov et al.
BIOPHYSICAL JOURNAL (2006)
Stability and dynamics of virus capsids described by coarse-grained modeling
Anton Arkhipov et al.
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Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations
V. A. Harmandaris et al.
MACROMOLECULES (2006)
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations
Kei-ichi Okazaki et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Molecular dynamics: Survey of methods for simulating the activity of proteins
Stewart A. Adcock et al.
CHEMICAL REVIEWS (2006)
Molecular dynamics simulations of outer-membrane protease T from E-coli based on a hybrid coarse-grained/atomistic potential
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JOURNAL OF PHYSICS-CONDENSED MATTER (2006)
Can conformational change be described by only a few normal modes?
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BIOPHYSICAL JOURNAL (2006)
Generalized correlation for biomolecular dynamics
OF Lange et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
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BIOPHYSICAL JOURNAL (2006)
Insertion and assembly of membrane proteins via simulation
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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
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JOURNAL OF CHEMICAL PHYSICS (2005)
Slow protein conformational dynamics from multiple experimental structures: The helix/sheet transition of arc repressor
RB Best et al.
STRUCTURE (2005)
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
E Villa et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
A multiscale coarse-graining method for biomolecular systems
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JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
A Liwo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
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JOURNAL OF MOLECULAR BIOLOGY (2005)
The protein folding 'speed limit'
J Kubelka et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
O Kurkcuoglu et al.
POLYMER (2004)
Complex folding pathways in a simple β-hairpin
GH Wei et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
An efficient hybrid explicit/implicit solvent method for biomolecular simulations
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JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
Deriving effective mesoscale potentials from atomistic simulations
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JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
The origins of asymmetry in the folding transition states of protein L and protein G
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PROTEIN SCIENCE (2002)
Dynamics of large proteins through hierarchical levels of coarse-grained structures
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JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
α-helix formation:: Discontinuous molecular dynamics on an intermediate-resolution protein model
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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2001)
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Conformational change of proteins arising from normal mode calculations
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PROTEIN ENGINEERING (2001)
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