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。An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations
Luitgard Nagel-Steger et al.
CHEMBIOCHEM (2016)
Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin
Yonathan Goldtzvik et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Advances in the Simulation of Protein Aggregation at the Atomistic Scale
Martin Carballo-Pacheco et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Evaluation of the coarse-grained OPEP force field for protein-protein docking
Philipp Kynast et al.
BMC BIOPHYSICS (2016)
Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies
Jessica Nasica-Labouze et al.
CHEMICAL REVIEWS (2015)
Inhibition of protein aggregation and amyloid formation by small molecules
Andrew J. Doig et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)
Molecular structure of the NQTrp inhibitor with the Alzheimer Aβ1-28 monomer
Bogdan Tarus et al.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2015)
Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics
Fabio Sterpone et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field
Maria Kalimeri et al.
JOURNAL OF NON-CRYSTALLINE SOLIDS (2015)
Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations
Bogdan Tarus et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering
Tong Zhang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
The physical basis of protein misfolding disorders
Tuomas P. J. Knowles et al.
PHYSICS TODAY (2015)
Hydrodynamic collective effects of active protein machines in solution and lipid bilayers
Alexander S. Mikhailov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Peptide dimer structure in an Aβ(1-42) fibril visualized with cryo-EM
Matthias Schmidt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Varied Probability of Staying Collapsed/Extended at the Conformational Equilibrium of Monomeric Aβ40 and Aβ42
Wanling Song et al.
SCIENTIFIC REPORTS (2015)
Understanding Amyloid Fibril Nucleation and Aβ Oligomer/Drug Interactions from Computer Simulations
Phuong Nguyent et al.
ACCOUNTS OF CHEMICAL RESEARCH (2014)
Significant Structural Differences between Transient Amyloid-β Oligomers and Less-Toxic Fibrils in Regions Known To Harbor Familial Alzheimer's Mutations
Bidyut Sarkar et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)
New Force Field on Modeling Intrinsically Disordered Proteins
Wei Wang et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2014)
Early amyloid β-protein aggregation precedes conformational change
Bogdan Barz et al.
CHEMICAL COMMUNICATIONS (2014)
Difference in dimer conformation between amyloid-β(1-42) and (1-43) proteins: Replica exchange molecular dynamics simulations in water
Atsushi Yano et al.
CHEMICAL PHYSICS LETTERS (2014)
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
Fabio Sterpone et al.
CHEMICAL SOCIETY REVIEWS (2014)
Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16-22 and Sup357-13 in AOT reverse micelles
Anna Victoria Martinez et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Effects of Macromolecular Crowding on Amyloid Beta (16-22) Aggregation Using Coarse-Grained Simulations
David C. Latshaw et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
A Kinetic Approach to the Sequence-Aggregation Relationship in Disease-Related Protein Assembly
Bogdan Barz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Simulations of Protein Aggregation: Insights from Atomistic and Coarse-Grained Models
Alex Morriss-Andrews et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Crucial role of nonspecific interactions in amyloid nucleation
Andela Saric et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Differences in nucleation behavior underlie the contrasting aggregation kinetics of the Aβ40 and Aβ42 peptides
Georg Meisl et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models
Tadashi Ando et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation
Tadashi Ando et al.
BIOPHYSICAL JOURNAL (2013)
Perspective: Reaches of chemical physics in biology
Martin Gruebele et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Improved Parameters for the Martini Coarse-Grained Protein Force Field
Djurre H. de Jong et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation
Fabio Sterpone et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach
David J. Rosenman et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's Aβ37-42 Amyloid Peptide Oligomers
Phuong H. Nguyen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Role of Water in Protein Aggregation and Amyloid Polymorphism
D. Thirumalai et al.
ACCOUNTS OF CHEMICAL RESEARCH (2012)
Effects of Familial Mutations on the Monomer Structure of Aβ42
Yu-Shan Lin et al.
BIOPHYSICAL JOURNAL (2012)
The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins
Yassmine Chebaro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
Fahimeh Baftizadeh et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation
Kresten Lindorff-Larsen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Atomic-level investigations on the amyloid-β dimerization process and its driving forces in water
Song-Ho Chong et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2012)
Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides
K. Aurelia Ball et al.
BIOCHEMISTRY (2011)
Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study
Robert Vacha et al.
BIOPHYSICAL JOURNAL (2011)
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer
Phuong H. Nguyen et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35
Jessica Nasica-Labouze et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association
Tamara Frembgen-Kesner et al.
BIOPHYSICAL JOURNAL (2010)
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
Tadashi Ando et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Extending the PRIME model for protein aggregation to all 20 amino acids
Mookyung Cheon et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Branching in Amyloid Fibril Growth
Christian Beyschau Andersen et al.
BIOPHYSICAL JOURNAL (2009)
MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations
M. Bernaschi et al.
COMPUTER PHYSICS COMMUNICATIONS (2009)
Hydrodynamic interactions in protein folding
Marek Cieplak et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Effect of β-sheet propensity on peptide aggregation
Giovanni Bellesia et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Diversity of kinetic pathways in amyloid fibril formation
Giovanni Bellesia et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Simulations of nucleation and elongation of amyloid fibrils
Jianing Zhang et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
Tamara Frembgen-Kesner et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Hydrodynamic Selection of the Kinetic Pathway of a Polymer Coil-Globule Transition
Kumiko Kamata et al.
PHYSICAL REVIEW LETTERS (2009)
Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent
Yan Lu et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Multiscale simulation of nanobiological flows
Maria Fyta et al.
COMPUTING IN SCIENCE & ENGINEERING (2008)
Self-assembly of the β2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals β-barrel species
Wei Song et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Facial symmetry in protein self-assembly
Anil K. Mehta et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: Theory and multiscale simulations
Maria Fyta et al.
PHYSICAL REVIEW E (2008)
A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates
Stefan Auer et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
A coarse-grained protein force field for folding and structure prediction
Julien Maupetit et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Branched chain mechanism of polymerization and ultrastructure of prion protein amyloid fibrils
Ilia V. Baskakov
FEBS JOURNAL (2007)
Design of quasisymplectic propagators for Langevin dynamics
Simone Melchionna
JOURNAL OF CHEMICAL PHYSICS (2007)
Fiber-dependent amyloid formation as catalysis of an existing reaction pathway
Amy M. Ruschak et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Stability and structure of oligomers of the Alzheimer peptide Aβ16-22:: From the dimer to the 32-mer
Ute F. Rohrig et al.
BIOPHYSICAL JOURNAL (2006)
Interpreting the aggregation kinetics of amyloid peptides
Riccardo Pellarin et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Lattice Boltzmann versus molecular dynamics simulation of nanoscale hydrodynamic flows
J Horbach et al.
PHYSICAL REVIEW LETTERS (2006)
Polymorphic fibril formation by residues 10-40 of the Alzheimer's β-amyloid peptide
Anant K. Paravastu et al.
BIOPHYSICAL JOURNAL (2006)
ESPResSo - an extensible simulation package for research on soft matter systems
HJ Limbach et al.
COMPUTER PHYSICS COMMUNICATIONS (2006)
Kinetic theory representation of hydrodynamics: a way beyond the Navier-Stokes equation
XW Shan et al.
JOURNAL OF FLUID MECHANICS (2006)
Following the aggregation of amyloid-forming peptides by computer simulations
A Melquiond et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Self-propagating, molecular-level polymorphism in Alzheimer's β-amyloid fibrils
AT Petkova et al.
SCIENCE (2005)
Techniques to study amyloid fibril formation in vitro
MR Nilsson
METHODS (2004)
Sampling the complex energy landscape of a simple β-hairpin
GH Wei et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Translational diffusion measured by PFG-NMR on full length and fragments of the Alzheimer Aβ(1-40) peptide.: Determination of hydrodynamic radii of random coil peptides of varying length
J Danielsson et al.
MAGNETIC RESONANCE IN CHEMISTRY (2002)
Discrete lattice effects on the forcing term in the lattice Boltzmann method
ZL Guo et al.
PHYSICAL REVIEW E (2002)
Computer simulations aimed at structure prediction of supersecondary motifs in proteins
F Forcellino et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2001)
Calculation of hydrodynamic properties of globular proteins from their atomic-level structure
JG de la Torre et al.
BIOPHYSICAL JOURNAL (2000)