- Home
- Publications
- Publication Search
- Publication Details
Title
The power of coarse graining in biomolecular simulations
Authors
Keywords
-
Journal
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume 4, Issue 3, Pages 225-248
Publisher
Wiley
Online
2013-08-27
DOI
10.1002/wcms.1169
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- 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
- Membrane Tension, Lipid Adaptation, Conformational Changes, and Energetics in MscL Gating
- (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
- Assessing the Quality of the OPEP Coarse-Grained Force Field
- (2011) Alessandro Barducci et al. Journal of Chemical Theory and Computation
- Using the Wimley–White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model
- (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
- A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
- (2011) Goundla Srinivas et al. Journal of Chemical Theory and Computation
- Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects
- (2011) Michel Masella et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
- (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
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search