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。Capturing Choline-Aromatics Cation-pi Interactions in the MARTINI Force Field
Hanif M. Khan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Protein-ligand binding with the coarse-grained Martini model
Paulo C. T. Souza et al.
NATURE COMMUNICATIONS (2020)
Temperature and Phase Transferable Bottom-up Coarse-Grained Models
Jaehyeok Jin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction
Luis Itza Vazquez-Salazar et al.
GREEN CHEMISTRY (2020)
Pitfalls of the Martini Model
Riccardo Alessandri et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation
Paulo C. T. Souza et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)
Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations
Svenja J. Woerner et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains
Jian Liu et al.
ADVANCED MATERIALS (2018)
Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association
Jan Domanski et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Transferable MARTINI Model of Poly(ethylene Oxide)
Fabian Grunewald et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Hydrodynamics of Diffusion in Lipid Membrane Simulations
Martin Voegele et al.
PHYSICAL REVIEW LETTERS (2018)
Ionic liquid ion exchange: exclusion from strong interactions condemns cations to the most weakly interacting anions and dictates reaction equilibrium
Pieter Naert et al.
GREEN CHEMISTRY (2018)
Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field
Timothy S. Carpenter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling
Hsin-Yung Yen et al.
NATURE (2018)
Biophysical experiments and biomolecular simulations: A perfect match?
Sandro Bottaro et al.
SCIENCE (2018)
A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions
Julian Michalowsky et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides
Philipp S. Schmalhorst et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
Adolfo B. Poma et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions
Halil I. Okur et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations
Riccardo Alessandri et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)
A tethering complex drives the terminal stage of SNARE-dependent membrane fusion
Massimo D'Agostino et al.
NATURE (2017)
Into the Dynamics of a Supramolecular Polymer at Submolecular Resolution
Davide Bochicchio et al.
NATURE COMMUNICATIONS (2017)
Electro-osmotic capture and ionic discrimination of peptide and protein biomarkers with FraC nanopores
Gang Huang et al.
NATURE COMMUNICATIONS (2017)
Mitochondria localization induced self-assembly of peptide amphiphiles for cellular dysfunction
M. T. Jeena et al.
NATURE COMMUNICATIONS (2017)
Stability and dynamics of membrane-spanning DNA nanopores
Vishal Maingi et al.
NATURE COMMUNICATIONS (2017)
Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex
Floris J. Van Eerden et al.
NATURE COMMUNICATIONS (2017)
Structural basis for maintenance of bacterial outer membrane lipid asymmetry
Javier Abellon-Ruiz et al.
NATURE MICROBIOLOGY (2017)
Excessive aggregation of membrane proteins in the Martini model
Matti Javanainen et al.
PLOS ONE (2017)
The role of hydrophobic matching on transmembrane helix packing in cells
Brayan Grau et al.
CELL STRESS (2017)
Martini Coarse-Grained Force Field: Extension to RNA
Jaakko J. Uusitalo et al.
BIOPHYSICAL JOURNAL (2017)
A Soluble, Folded Protein without Charged Amino Acid Residues
Casper Hojgaard et al.
BIOCHEMISTRY (2016)
Martini straight: Boosting performance using a shorter cutoff and GPUs
Djurre H. de Jong et al.
COMPUTER PHYSICS COMMUNICATIONS (2016)
On the representability problem and the physical meaning of coarse-grained models
Jacob W. Wagner et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Improved Side Chain Dynamics in MARTINI Simulations of Protein Lipid Interfaces
Florian A. Herzog et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
De novo design of transmembrane helix-helix interactions and measurement of stability in a biological membrane
Anthony Nash et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2015)
The impact of resolution upon entropy and information in coarse-grained models
Thomas T. Foley et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Parameters for Martini sterols and hopanoids based on a virtual-site description
M. N. Melo et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach
Tsjerk A. Wassenaar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Martini Coarse-Grained Force Field: Extension to DNA
Jaakko J. Uusitalo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
Tsjerk A. Wassenaar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Overview of the Effect of Salts on Biphasic Ionic Liquid/Water Solvent Extraction Systems: Anion Exchange, Mutual Solubility, and Thermomorphic Properties
David Dupont et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Crystal Structure of the Glycophorin A Transmembrane Dimer in Lipidic Cubic Phase
Raphael Trenker et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Subnanometre ligand-shell asymmetry leads to Janus-like nanoparticle membranes
Zhang Jiang et al.
NATURE MATERIALS (2015)
Structural basis for self-assembly of a cytolytic pore lined by protein and lipid
Koji Tanaka et al.
NATURE COMMUNICATIONS (2015)
Exploring the sequence space for (tri-) peptide self-assembly to design and discover
Pim W. J. M. Frederix et al.
NATURE CHEMISTRY (2015)
The power of coarse graining in biomolecular simulations
Helgi I. Ingolfsson et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)
Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
Drazen Petrov et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Glycophorin A transmembrane domain dimerization in plasma membrane vesicles derived from CHO, HEK 293T, and A431 cells
Sarvenaz Sarabipour et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2013)
Perspective on the Martini model
Siewert J. Marrink et al.
CHEMICAL SOCIETY REVIEWS (2013)
A flexible algorithm for calculating pair interactions on SIMD architectures
Szilard Pall et al.
COMPUTER PHYSICS COMMUNICATIONS (2013)
Improved Parameters for the Martini Coarse-Grained Protein Force Field
Djurre H. de Jong et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Toward Optimized Potential Functions for Protein-Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field
Austin C. Stark et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Martini Force Field Parameters for Glycolipids
Cesar A. Lopez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations
Tsjerk A. Wassenaar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
Wei Liu et al.
SCIENCE (2012)
Driving Force for the Association of Hydrophobic Peptides: The Importance of Electrostatic Interactions in Coarse-Grained Water Models
Zhe Wu et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)
Kirkwood-Buff integrals for ideal solutions
Elizabeth A. Ploetz et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Measuring the Energetics of Membrane Protein Dimerization in Mammalian Membranes
Lirong Chen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Method to measure strong protein-protein interactions in lipid bilayers using a steric trap
Heedeok Hong et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Polarizable Water Model for the Coarse-Grained MARTINI Force Field
Semen O. Yesylevskyy et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Energetics of ErbB1 Transmembrane Domain Dimerization in Lipid Bilayers
Lirong Chen et al.
BIOPHYSICAL JOURNAL (2009)
Martini Coarse-Grained Force Field: Extension to Carbohydrates
Cesar A. Lopez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
Xavier Periole et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Simultaneous use of small- and wide-angle X-ray techniques to analyze nanometerscale phase separation in polymer heterojunction solar cells
Mao-Yuan Chiu et al.
ADVANCED MATERIALS (2008)
Transmembrane domain of EphA1 receptor forms dimers in membrane-like environment
Elena O. Artemenko et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2008)
The MARTINI coarse-grained force field: Extension to proteins
Luca Monticelli et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Multiscale coarse-graining and structural correlations: Connections to liquid-state theory
W. G. Noid et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Effect of salts and organic additives on the solubility of proteins in aqueous solutions
Eli Ruckenstein et al.
ADVANCES IN COLLOID AND INTERFACE SCIENCE (2006)
The stability of transmembrane helix interactions measured in a biological membrane
Carmen Finger et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Self-association of transmembrane α-helices in model membranes -: Importance of helix orientation and role of hydrophobic mismatch
E Sparr et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2005)
Coarse grained model for semiquantitative lipid simulations
SJ Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Aromatic oligomers that form hetero duplexes in aqueous solution
GJ Gabriel et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Polar residues drive association of polyleucine transmembrane helices
FX Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Phosphothreonine recognition comes into focus
MM Zhou
NATURE STRUCTURAL BIOLOGY (2000)
Synthesis and conformational characterization of tethered, self-complexing 1,5-dialkoxynaphthalene/1,4,5,8-naphthalenetetracarboxylic diimide systems
AJ Zych et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)
Allosteric modulation of A2A adenosine receptors by amiloride analogues and sodium ions
ZG Gao et al.
BIOCHEMICAL PHARMACOLOGY (2000)