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。Macromolecular Crowding Is More than Hard-Core Repulsions
Shannon L. Speer et al.
ANNUAL REVIEW OF BIOPHYSICS (2022)
Improving Martini 3 for Disordered and Multidomain Proteins
F. Emil Thomasen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)
Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Cheng Tan et al.
PLOS COMPUTATIONAL BIOLOGY (2022)
Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein
Takaharu Mori et al.
BIOPHYSICAL JOURNAL (2021)
Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase
Chigusa Kobayashi et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Physics-based computational and theoretical approaches to intrinsically disordered proteins
Joan-Emma Shea et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)
Systematic design of biomolecular force fields
David van der Spoel
CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)
A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins
Thomas Dannenhoffer-Lafage et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins
Roshan Mammen Regy et al.
PROTEIN SCIENCE (2021)
Optimized Hydrogen Mass Repartitioning Scheme Combined with Accurate Temperature/Pressure Evaluations for Thermodynamic and Kinetic Properties of Biological Systems
Jaewoon Jung et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space
Chao Lu et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants
Abhinaw Kumar et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)
Reduced efficacy of a Src kinase inhibitor in crowded protein solution
Kento Kasahara et al.
NATURE COMMUNICATIONS (2021)
Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy
Jerelle A. Joseph et al.
NATURE COMPUTATIONAL SCIENCE (2021)
Biomolecular modeling thrives in the age of technology
Tamar Schlick et al.
NATURE COMPUTATIONAL SCIENCE (2021)
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
Chuan Tian et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
TDP-43 α-helical structure tunes liquid-liquid phase separation and function
Alexander E. Conicella et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins
Wai Shing Tang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2020)
Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations
Wenwei Zheng et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2020)
PROTEIN MODELING Protein storytelling through physics
Emiliano Brini et al.
SCIENCE (2020)
Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties
Gul H. Zerze et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)
Dynamic cluster formation determines viscosity and diffusion in dense protein solutions
Soeron von Buelow et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Molecular interactions underlying liquid-liquid phase separation of the FUS low-complexity domain
Anastasia C. Murthy et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)
Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules
Hiraku Oshima et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
In-Cell Protein-Protein Contacts: Transient Interactions in the Crowd
Meredith M. Rickard et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)
Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape
Suyong Re et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer
Viet Hoang Man et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Developing a molecular dynamics force field for both folded and disordered protein states
Paul Robustelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Sequence determinants of protein phase behavior from a coarse-grained model
Gregory L. Dignon et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Mechanism of NMDA receptor channel block by MK-801 and memantine
Xianqiang Song et al.
NATURE (2018)
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Jing Huang et al.
NATURE METHODS (2017)
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
Chigusa Kobayashi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation
Grzegorz Nawrocki et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Crowding in Cellular Environments at an Atomistic Level from Computer Simulations
Michael Feig et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field
Hao-Nan Wu et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)
Water is an active matrix of life for cell and molecular biology
Philip Ball
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
Yinglong Miao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
Stefano Piana et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
Jaewoon Jung et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)
A series of PDB-related databanks for everyday needs
Wouter G. Touw et al.
NUCLEIC ACIDS RESEARCH (2015)
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)
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
Robert B. Best et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
Ryuhei Harada et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Biomolecular Simulation: A Computational Microscope for Molecular Biology
Ron O. Dror et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)
Residue-Specific α-Helix Propensities from Molecular Simulation
Robert B. Best et al.
BIOPHYSICAL JOURNAL (2012)
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles
Robert B. Best et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Optimizing Solute-Water van der Waals Interactions To Reproduce Solvation Free Energies
Paul S. Nerenberg et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Protein Crowding Affects Hydration Structure and Dynamics
Ryuhei Harada et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models
A. Ortega et al.
BIOPHYSICAL JOURNAL (2011)
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
Stefano Piana et al.
BIOPHYSICAL JOURNAL (2011)
Protein Crowding Tunes Protein Stability
Andrew C. Miklos et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Spontaneous formation of the unlocked state of the ribosome is a multistep process
James B. Munro et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining
Kristina M Hettne et al.
Journal of Cheminformatics (2010)
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
Huan-Xiang Zhou et al.
ANNUAL REVIEW OF BIOPHYSICS (2008)
Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
A temperature predictor for parallel tempering simulations
Alexandra Patriksson et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Folding free-energy landscape of a 10-residue mini-protein, chignolin
Daisuke Satoh et al.
FEBS LETTERS (2006)
A general purpose model for the condensed phases of water: TIP4P/2005
JLF Abascal et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
The crystal structure of a c-Src complex in an active conformation suggests possible steps in c-Src activation
SW Cowan-Jacob et al.
STRUCTURE (2005)
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
AD Mackerell et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
10 residue folded peptide designed by segment statistics
S Honda et al.
STRUCTURE (2004)
System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions
IC Yeh et al.
JOURNAL OF PHYSICAL CHEMISTRY B (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)
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
MR Shirts et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Multidimensional replica-exchange method for free-energy calculations
Y Sugita et al.
JOURNAL OF CHEMICAL PHYSICS (2000)