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。Facilitating CG Simulations with MAD: The MArtini Database Server
Cecile Hilpert et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2023)
Two decades of Martini: Better beads, broader scope
Siewert J. Marrink et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2023)
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
Abigail Dommer et al.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2023)
Fundamental behaviors emerge from simulations of a living minimal cell
Zane R. Thornburg et al.
CELL (2022)
Assembly and Analysis of Cell-Scale Membrane Envelopes
Josh V. Vermaas et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)
Building Structural Models of a Whole Mycoplasma Cell
Martina Maritan et al.
JOURNAL OF MOLECULAR BIOLOGY (2022)
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials
Fabian Grunewald et al.
NATURE COMMUNICATIONS (2022)
Martini 3 Coarse-Grained Force Field: Small Molecules
Riccardo Alessandri et al.
ADVANCED THEORY AND SIMULATIONS (2022)
The ugly, bad, and good stories of large-scale biomolecular simulations
Chitrak Gupta et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)
Martini 3 Coarse-Grained Force Field for Carbohydrates
Fabian Grunewald et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)
Integrating cellular and molecular structures and dynamics into whole-cell models
Zaida Luthey-Schulten et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)
Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework
Cesar A. Lopez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)
AI-based structure prediction empowers integrative structural analysis of human nuclear pores
Shyamal Mosalaganti et al.
SCIENCE (2022)
Toward the Complete Functional Characterization of a Minimal Bacterial Proteome
David M. Bianchi et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2022)
Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies
Filipe M. Sousa et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies
Bart M. H. Bruininks et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
GLIMPS: A Machine Learning Approach to Resolution Transformation for Multiscale Modeling
Keverne A. Louison et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope
Roman Schmidt et al.
NATURE COMMUNICATIONS (2021)
Martini 3: a general purpose force field for coarse-grained molecular dynamics
Paulo C. T. Souza et al.
NATURE METHODS (2021)
Integrating experiments, theory and simulations into whole-cell models
Zaida Luthey-Schulten
NATURE METHODS (2021)
50 years of PBD: a catalyst in structural biology
Alexandre M. J. J. Bonvin
NATURE METHODS (2021)
Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning
Thomas D. Potter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations
Owen N. Vickery et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Highly accurate protein structure prediction with AlphaFold
John Jumper et al.
NATURE (2021)
Towards a synthetic cell cycle
Lorenzo Olivi et al.
NATURE COMMUNICATIONS (2021)
Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps
Benjamin R. Gilbert et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2021)
Whole-Cell Modeling and Simulation: A Brief Survey
Nayana G. Bhat et al.
NEW GENERATION COMPUTING (2020)
RNA Droplets
Kevin Rhine et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 49, 2020 (2020)
Machine Learning for Molecular Simulation
Frank Noé et al.
Annual Review of Physical Chemistry (2020)
Towards extreme scale dissipative particle dynamics simulations using multiple GPGPUs
Jony Castagna et al.
COMPUTER PHYSICS COMMUNICATIONS (2020)
Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation
Leandro Oliveira Bortot et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Resolving Membrane Protein-Protein Interactions in Live Cells with Pulsed Interleaved Excitation Fluorescence Cross-Correlation Spectroscopy
Shaun Christie et al.
ACCOUNTS OF CHEMICAL RESEARCH (2020)
Machine learning approaches for analyzing and enhancing molecular dynamics simulations
Yihang Wang et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Simulation of subcellular structures
Syma Khalid et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Backmapping triangulated surfaces to coarse-grained membrane models
Weria Pezeshkian et al.
NATURE COMMUNICATIONS (2020)
When Small becomes Too Big: Expanding the Use of In-Cell Solid-State NMR Spectroscopy
Siddarth Narasimhan et al.
CHEMPLUSCHEM (2020)
Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision
Wojciech Wietrzynski et al.
ELIFE (2020)
Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape
J. H. Lorent et al.
NATURE CHEMICAL BIOLOGY (2020)
ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field
Xiaohua Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo
Martin Stefl et al.
BIOPHYSICAL JOURNAL (2020)
ATP-Driven Separation of Liquid Phase Condensates in Bacteria
Baptiste Guilhas et al.
MOLECULAR CELL (2020)
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
Derek N. Macklin et al.
SCIENCE (2020)
Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations
Jaewoon Jung et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2019)
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism
Abhishek Singharoy et al.
CELL (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)
Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending
Grzegorz Nawrocki et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Computational Modeling of Realistic Cell Membranes
Siewert J. Marrink et al.
CHEMICAL REVIEWS (2019)
MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution
Yvan Eilers et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins
Valentina Corradi et al.
ACS CENTRAL SCIENCE (2018)
The 2018 correlative microscopy techniques roadmap
Toshio Ando et al.
JOURNAL OF PHYSICS D-APPLIED PHYSICS (2018)
Single-particle cryo-EM-How did it get here and where will it go
Yifan Cheng
SCIENCE (2018)
Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry
Dror S. Chorev et al.
SCIENCE (2018)
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)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Interrogating Membrane Protein Conformational Dynamics within Native Lipid Compositions
Eamonn Reading et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)
Martini Coarse-Grained Force Field: Extension to RNA
Jaakko J. Uusitalo et al.
BIOPHYSICAL JOURNAL (2017)
Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units
Michael P. Howard et al.
COMPUTER PHYSICS COMMUNICATIONS (2016)
Design and synthesis of a minimal bacterial genome
Clyde A. Hutchison et al.
SCIENCE (2016)
The principles of whole-cell modeling
Jonathan R. Karr et al.
CURRENT OPINION IN MICROBIOLOGY (2015)
Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules
Tristan Bereau 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)
cellPACK: a virtual mesoscope to model and visualize structural systems biology
Graham T. Johnson et al.
NATURE METHODS (2015)
The future of whole-cell modeling
Derek N. Macklin et al.
CURRENT OPINION IN BIOTECHNOLOGY (2014)
Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
C. A. Brackley et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Improved Parameters for the Martini Coarse-Grained Protein Force Field
Djurre H. de Jong et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Lattice Microbes: High-Performance Stochastic Simulation Method for the Reaction-Diffusion Master Equation
Elijah Roberts et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Biomolecular Simulation: A Computational Microscope for Molecular Biology
Ron O. Dror et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Jonathan R. Karr et al.
CELL (2012)
Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells
Jagannath Mondal et al.
BIOPHYSICAL JOURNAL (2011)
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
Sean R. McGuffee et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Martini Coarse-Grained Force Field: Extension to Carbohydrates
Cesar A. Lopez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Discovery Through the Computational Microscope
Eric H. Lee et al.
STRUCTURE (2009)
Computation of rotation minimizing frames
Wenping Wang et al.
ACM TRANSACTIONS ON GRAPHICS (2008)