标题
The power of coarse graining in biomolecular simulations
作者
关键词
-
出版物
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume 4, Issue 3, Pages 225-248
出版商
Wiley
发表日期
2013-08-27
DOI
10.1002/wcms.1169
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues
- (2013) Katharina Meier et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Does Microsecond Sugar Ring Flexing Encode 3D-Shape and Bioactivity in the Heparanome?
- (2013) Benedict M. Sattelle et al. BIOMACROMOLECULES
- Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose
- (2013) Sergiy Markutsya et al. JOURNAL OF CHEMICAL PHYSICS
- MagiC: Software Package for Multiscale Modeling
- (2013) Alexander Mirzoev et al. Journal of Chemical Theory and Computation
- PRIMO: A Transferable Coarse-Grained Force Field for Proteins
- (2013) Parimal Kar et al. Journal of Chemical Theory and Computation
- Martini Force Field Parameters for Glycolipids
- (2013) César A. López et al. Journal of Chemical Theory and Computation
- Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations
- (2013) Tsjerk A. Wassenaar et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular Dynamics Simulations of DPPC Bilayers Using “LIME”, a New Coarse-Grained Model
- (2013) Emily M. Curtis et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation
- (2013) Christoph Globisch et al. PLoS One
- Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels
- (2013) C. Arnarez et al. Scientific Reports
- Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes
- (2013) Cesar A. López et al. Scientific Reports
- Biomolecular Simulation: A Computational Microscope for Molecular Biology
- (2012) Ron O. Dror et al. Annual Review of Biophysics
- Molecular Structure of Membrane Tethers
- (2012) Svetlana Baoukina et al. BIOPHYSICAL JOURNAL
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- (2012) Petr Šulc et al. JOURNAL OF CHEMICAL PHYSICS
- Chemically transferable coarse-grained potentials from conditional reversible work calculations
- (2012) E. Brini et al. JOURNAL OF CHEMICAL PHYSICS
- Modeling Protein–Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION
- (2012) Nathalie Basdevant et al. Journal of Chemical Theory and Computation
- Solvent Free Ionic Solution Models from Multiscale Coarse-Graining
- (2012) Zhen Cao et al. Journal of Chemical Theory and Computation
- BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores
- (2012) Pablo M. De Biase et al. Journal of Chemical Theory and Computation
- PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties
- (2012) Marco Pasi et al. Journal of Chemical Theory and Computation
- Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains
- (2012) Wei Han et al. Journal of Chemical Theory and Computation
- Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields
- (2012) Djurre H. de Jong et al. Journal of Chemical Theory and Computation
- Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk
- (2012) Leonardo Darré et al. Journal of Chemical Theory and Computation
- Hybrid Approach for Highly Coarse-Grained Lipid Bilayer Models
- (2012) Anand Srivastava et al. Journal of Chemical Theory and Computation
- Improved Parameters for the Martini Coarse-Grained Protein Force Field
- (2012) Djurre H. de Jong et al. Journal of Chemical Theory and Computation
- Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose
- (2012) Giovanni Bellesia et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins
- (2012) Yassmine Chebaro et al. JOURNAL OF PHYSICAL CHEMISTRY B
- AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
- (2012) Aram Davtyan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Understanding the Phase Behavior of Coarse-Grained Model Lipid Bilayers through Computational Calorimetry
- (2012) Jocelyn M. Rodgers et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers
- (2012) Xavier Periole et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Coarse-grained molecular models of water: a review
- (2012) Kevin R. Hadley et al. MOLECULAR SIMULATION
- Predictive energy landscapes for protein-protein association
- (2012) W. Zheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Systematic coarse-graining methods for soft matter simulations – a review
- (2012) Emiliano Brini et al. Soft Matter
- Recent successes in coarse-grained modeling of DNA
- (2012) Davit A. Potoyan et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Coarse-grained models of water
- (2012) Leonardo Darré et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites
- (2011) Juan J. de Pablo Annual Review of Physical Chemistry
- Transmembrane helices can induce domain formation in crowded model membranes
- (2011) Jan Domański et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- In Silico Design of Robust Bolalipid Membranes
- (2011) Monica Bulacu et al. BIOMACROMOLECULES
- Protein Shape Change Has a Major Effect on the Gating Energy of a Mechanosensitive Channel
- (2011) O.H. Samuli Ollila et al. BIOPHYSICAL JOURNAL
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- (2011) Huan Rui et al. BIOPHYSICAL JOURNAL
- Computational approaches to RNA structure prediction, analysis, and design
- (2011) Christian Laing et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Moving beyond Watson–Crick models of coarse grained DNA dynamics
- (2011) Margaret C. Linak et al. JOURNAL OF CHEMICAL PHYSICS
- A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations
- (2011) Sereina Riniker et al. JOURNAL OF CHEMICAL PHYSICS
- Coarse-graining errors and numerical optimization using a relative entropy framework
- (2011) Aviel Chaimovich et al. JOURNAL OF CHEMICAL PHYSICS
- Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
- (2011) Thomas E. Ouldridge et al. JOURNAL OF CHEMICAL PHYSICS
- A coarse-grain three-site-per-nucleotide model for DNA with explicit ions
- (2011) Gordon S. Freeman et al. JOURNAL OF CHEMICAL PHYSICS
- From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
- (2011) Phillip J. Stansfeld et al. Journal of Chemical Theory and Computation
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- (2011) Alessandro Barducci et al. Journal of Chemical Theory and Computation
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- (2011) Gurpreet Singh et al. Journal of Chemical Theory and Computation
- A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose
- (2011) Jakob Wohlert et al. Journal of Chemical Theory and Computation
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- (2011) Goundla Srinivas et al. Journal of Chemical Theory and Computation
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- (2011) Michel Masella et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
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- (2011) Bram van Hoof et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
- (2011) Andrzej J. Rzepiela et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Multiscale modeling of biological functions
- (2011) Shina Caroline Lynn Kamerlin et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Coarse-grained force field: general folding theory
- (2011) Adam Liwo et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
- (2011) L. V. Schafer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- How Fast-Folding Proteins Fold
- (2011) K. Lindorff-Larsen et al. SCIENCE
- Capturing the essence of folding and functions of biomolecules using coarse-grained models
- (2011) Changbong Hyeon et al. Nature Communications
- A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
- (2010) Alex Morriss-Andrews et al. JOURNAL OF CHEMICAL PHYSICS
- An implicit solvent coarse-grained lipid model with correct stress profile
- (2010) Alex J. Sodt et al. JOURNAL OF CHEMICAL PHYSICS
- A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics
- (2010) Pablo D. Dans et al. Journal of Chemical Theory and Computation
- A Coarse-Grained Model Based on Morse Potential for Water andn-Alkanes
- (2010) See-Wing Chiu et al. Journal of Chemical Theory and Computation
- Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?
- (2010) Leonardo Darré et al. Journal of Chemical Theory and Computation
- Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field
- (2010) Ana Rojas et al. JOURNAL OF MOLECULAR BIOLOGY
- PDZ Binding to the BAR Domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics
- (2010) Yi He et al. JOURNAL OF MOLECULAR BIOLOGY
- Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
- (2010) Gia G. Maisuradze et al. JOURNAL OF PHYSICAL CHEMISTRY A
- A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions
- (2010) Zhe Wu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- On the Investigation of Coarse-Grained Models for Water: Balancing Computational Efficiency and the Retention of Structural Properties
- (2010) Kevin R. Hadley et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures
- (2010) Zhen Xia et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field
- (2010) Wataru Shinoda et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations
- (2010) Zun-Jing Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA
- (2010) Samuela Pasquali et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions
- (2010) Robert C. DeMille et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity
- (2010) Tristan Bereau et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Exploring the utility of coarse-grained water models for computational studies of interfacial systems
- (2010) Xibing He et al. MOLECULAR PHYSICS
- Recent progress in adaptive multiscale molecular dynamics simulations of soft matter
- (2010) Steven O. Nielsen et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
- (2010) Thomas E. Ouldridge et al. PHYSICAL REVIEW LETTERS
- Release of content through mechano-sensitive gates in pressurized liposomes
- (2010) M. Louhivuori et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nanoscale carbon particles and the stability of lipid bilayers
- (2010) Arben Jusufi et al. Soft Matter
- Recent development in computer simulations of lipid bilayers
- (2010) Alexander P. Lyubartsev et al. Soft Matter
- Polarizable Water Model for the Coarse-Grained MARTINI Force Field
- (2010) Semen O. Yesylevskyy et al. PLoS Computational Biology
- A Mesoscale Model of DNA and Its Renaturation
- (2009) E.J. Sambriski et al. BIOPHYSICAL JOURNAL
- Coarse-grained modeling of lipids
- (2009) Sandra V. Bennun et al. CHEMISTRY AND PHYSICS OF LIPIDS
- Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
- (2009) Han Wang et al. EUROPEAN PHYSICAL JOURNAL E
- Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
- (2009) Ronald Hills et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials
- (2009) Robert C. DeMille et al. JOURNAL OF CHEMICAL PHYSICS
- Extended ensemble approach for deriving transferable coarse-grained potentials
- (2009) J. W. Mullinax et al. JOURNAL OF CHEMICAL PHYSICS
- Generic coarse-grained model for protein folding and aggregation
- (2009) Tristan Bereau et al. JOURNAL OF CHEMICAL PHYSICS
- Martini Coarse-Grained Force Field: Extension to Carbohydrates
- (2009) Cesar A. López et al. Journal of Chemical Theory and Computation
- Versatile Object-Oriented Toolkit for Coarse-Graining Applications
- (2009) Victor Rühle et al. Journal of Chemical Theory and Computation
- Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
- (2009) Xavier Periole et al. Journal of Chemical Theory and Computation
- Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales
- (2009) Gary S. Ayton et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Systematic Coarse-graining of a Multicomponent Lipid Bilayer
- (2009) Lanyuan Lu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Mesoscopic Membrane Physics: Concepts, Simulations, and Selected Applications
- (2009) Markus Deserno MACROMOLECULAR RAPID COMMUNICATIONS
- Multiscale modeling of emergent materials: biological and soft matter
- (2009) Teemu Murtola et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis
- (2009) E. J. Sambriski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Effect of cholesterol on the structure of a phospholipid bilayer
- (2009) F. de Meyer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Multiscale characterization of protein conformational ensembles
- (2009) Amarda Shehu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
- (2009) Srinivasa M. Gopal et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back
- (2009) Christine Peter et al. Soft Matter
- Discovery Through the Computational Microscope
- (2009) Eric H. Lee et al. STRUCTURE
- Mechanosensitive Membrane Channels in Action
- (2008) Serge Yefimov et al. BIOPHYSICAL JOURNAL
- A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules
- (2008) Zhiyong Zhang et al. BIOPHYSICAL JOURNAL
- A polarizable coarse-grained water model for coarse-grained proteins simulations
- (2008) Tap Ha-Duong et al. CHEMICAL PHYSICS LETTERS
- The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
- (2008) W. G. Noid et al. JOURNAL OF CHEMICAL PHYSICS
- The MARTINI Coarse-Grained Force Field: Extension to Proteins
- (2008) Luca Monticelli et al. Journal of Chemical Theory and Computation
- Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent
- (2008) Yassmine Chebaro et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Water Modeled As an Intermediate Element between Carbon and Silicon†
- (2008) Valeria Molinero et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The molecular face of lipid rafts in model membranes
- (2008) H. J. Risselada et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
- (2008) F. Ding et al. RNA
- Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations
- (2007) Julien Michel et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Quantitative Coarse-Grain Model for Lipid Bilayers
- (2007) Mario Orsi et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Cholesterol Shows Preference for the Interior of Polyunsaturated Lipid Membranes
- (2007) Siewert J. Marrink et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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