相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Design and application of implicit solvent models in biomolecular simulations
Jens Kleinjung et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
Stefano Piana et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Hydration shells of proteins probed by depolarized light scattering and dielectric spectroscopy: Orientational structure is significant, positional structure is not
Daniel R. Martin et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Resolving anisotropic distributions of correlated vibrational motion in protein hydration water
Matthias Heyden
JOURNAL OF CHEMICAL PHYSICS (2014)
Adaptive resolution simulation of an atomistic protein in MARTINI water
Julija Zavadlav et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Chemical potential of liquids and mixtures via adaptive resolution simulation
Animesh Agarwal et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization
Jibao Lu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
Aoife C. Fogarty et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Transferable Coarse-Grained Potential for De Novo Protein Folding and Design
Ivan Coluzza
PLOS ONE (2014)
The power of coarse graining in biomolecular simulations
Helgi I. Ingolfsson et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)
The PDB_REDO server for macromolecular structure model optimization
Robbie P. Joosten et al.
IUCRJ (2014)
Solid-State NMR Approaches to Internal Dynamics of Proteins: From Picoseconds to Microseconds and Seconds
Alexey Krushelnitsky et al.
ACCOUNTS OF CHEMICAL RESEARCH (2013)
Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues
Katharina Meier et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)
Biomolecular hydration dynamics: a jump model perspective
Aoife C. Fogarty et al.
CHEMICAL SOCIETY REVIEWS (2013)
ESPResSo++: A modern multiscale simulation package for soft matter systems
Jonathan D. Halverson et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Finite domain simulations with adaptive boundaries: Accurate potentials and nonequilibrium movesets
Jason A. Wagoner et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Predicting the thermodynamics by using state-dependent interactions
Giuseppe D'Adamo et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
On the 'Dielectric Constant of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi
Lin Li et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Hybrid continuum-particle method for fluctuating lipid bilayer membranes with diffusing protein inclusions
Jon K. Sigurdsson et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2013)
Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations
Tsjerk A. Wassenaar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Nanosecond Time Scale Motions in Proteins Revealed by High-Resolution NMR Relaxometry
Cyril Charlier et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Coil-Globule-Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir
Debashish Mukherji et al.
MACROMOLECULES (2013)
Anomalous Anisotropic Diffusion Dynamics of Hydration Water at Lipid Membranes
Yann von Hansen et al.
PHYSICAL REVIEW LETTERS (2013)
Hamiltonian Adaptive Resolution Simulation for Molecular Liquids
Raffaello Potestio et al.
PHYSICAL REVIEW LETTERS (2013)
Long-range protein-water dynamics in hyperactive insect antifreeze proteins
Konrad Meister et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Grand-Canonical-like Molecular-Dynamics Simulations by Using an Adaptive-Resolution Technique
Han Wang et al.
PHYSICAL REVIEW X (2013)
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations
Sereina Riniker et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2012)
Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains
Wei Han et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Structure Formation of Toluene around C60: Implementation of the Adaptive Resolution Scheme (AdResS) into GROMACS
Sebastian Fritsch et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
Elio A. Cino et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations
Alexander V. Predeus et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water
Sereina Riniker et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
Rasmus Wedberg et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Site-Specific Hydration Dynamics of Globular Proteins and the Role of Constrained Water in Solvent Exchange with Amphiphilic Cosolvents
John T. King et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Magnitude and Molecular Origin of Water Slowdown Next to a Protein
Fabio Sterpone et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Coarse-grained molecular models of water: a review
Kevin R. Hadley et al.
MOLECULAR SIMULATION (2012)
Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir
S. Fritsch et al.
PHYSICAL REVIEW LETTERS (2012)
Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes
Michael Leguebe et al.
PLOS ONE (2012)
The Protein-Folding Problem, 50 Years On
Ken A. Dill et al.
SCIENCE (2012)
Structure of hydration water in proteins: A comparison of molecular dynamics simulations and database analysis
Nicholus Bhattacharjee et al.
BIOPHYSICAL CHEMISTRY (2011)
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
Thomas E. Ouldridge et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Dynamics of Water in Concentrated Solutions of Amphiphiles: Key Roles of Local Structure and Aggregation
Guillaume Stirnemann et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
A hybrid all-atom/coarse grain model for multiscale simulations of DNA
Matias Rodrigo Machado et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Multiscale Modeling of Proteins
Valentina Tozzini
ACCOUNTS OF CHEMICAL RESEARCH (2010)
Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA
Lukasz Szyc et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)
Global and local Voronoi analysis of solvation shells of proteins
Gregor Neumayr et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides
Manish Agarwal et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
Robbie P. Joosten et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2009)
Force Field Bias in Protein Folding Simulations
Peter L. Freddolino et al.
BIOPHYSICAL JOURNAL (2009)
Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
Han Wang et al.
EUROPEAN PHYSICAL JOURNAL E (2009)
The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin
Benjamin Born et al.
FARADAY DISCUSSIONS (2009)
Generic coarse-grained model for protein folding and aggregation
Tristan Bereau et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Versatile Object-Oriented Toolkit for Coarse-Graining Applications
Victor Ruehle et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Refinement of the Primary Hydration Shell Model for Molecular Dynamics Simulations of Large Proteins
Mehdi Bagheri Hamaneh et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Multiscale simulation of soft matter: From scale bridging to adaptive resolution
Matej Praprotnik et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY (2008)
Dynamics at the protein-water interface from 17O spin relaxation in deeply supercooled solutions
Carlos Mattea et al.
BIOPHYSICAL JOURNAL (2008)
Water as an active constituent in cell biology
Philip Ball
CHEMICAL REVIEWS (2008)
Modeling diffusive dynamics in adaptive resolution simulation of liquid water
Silvina Matysiak et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
On the Molecular Mechanism of Water Reorientation
Damien Laage et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
On the molecular mechanism of drug intercalation into DNA: A simulation study of the intercalation pathway, free energy, and DNA structural changes
Arnab Mukherjee et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
A coarse-grained protein force field for folding and structure prediction
Julien Maupetit et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Adaptive resolution simulation of liquid water
Matej Praprotnik et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2007)
PDB improvement starts with data deposition
Robbie P. Joosten et al.
SCIENCE (2007)
Representability problems for coarse-grained water potentials
Margaret E. Johnson et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
Qiang Shi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
M Praprotnik et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Coarse-grained model of proteins incorporating atomistic detail of the active site
M Neri et al.
PHYSICAL REVIEW LETTERS (2005)
Enzyme activity and flexibility at very low hydration
V Kurkal et al.
BIOPHYSICAL JOURNAL (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)
Coarse-grained models for proteins
V Tozzini
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
Recent advances in the development and application of implicit solvent models in biomolecule simulations
M Feig et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Protein hydration dynamics in solution: a critical survey
B Halle
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2004)
Ubiquitin: structures, functions, mechanisms
CM Pickart et al.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2004)
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Y Duan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Deriving effective mesoscale potentials from atomistic simulations
D Reith et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Structural and dynamic properties of water around acetylcholinesterase
RH Henchman et al.
PROTEIN SCIENCE (2002)
Beware of density dependent pair potentials
AA Louis
JOURNAL OF PHYSICS-CONDENSED MATTER (2002)
Statistical mechanical models with effective potentials: Definitions, applications, and thermodynamic consequences
FH Stillinger et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Water rotational relaxation and diffusion in hydrated lysozyme
M Marchi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Is the first hydration shell of lysozyme of higher density than bulk water?
F Merzel et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Relationship between structural order and the anomalies of liquid water
JR Errington et al.
NATURE (2001)
Improving enzymes by using them in organic solvents
AM Klibanov
NATURE (2001)