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。Resolution exchange with tunneling for enhanced sampling of protein landscapes
Fatih Yasar et al.
PHYSICAL REVIEW E (2022)
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
David Sehnal et al.
NUCLEIC ACIDS RESEARCH (2021)
High-resolution structure and strain comparison of infectious mammalian prions
Allison Kraus et al.
MOLECULAR CELL (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)
Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations
Hoang Linh Nguyen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2019)
Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ
Ana V. Rojas et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields
Adam K. Sieradzan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2018)
Mutations Alter RNA-Mediated Conversion of Human Prions
Erik J. Alred et al.
ACS OMEGA (2018)
Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics
Ana Rojas et al.
ACS CHEMICAL NEUROSCIENCE (2017)
Fatal familial insomnia: mitochondrial and protein synthesis machinery decline in the mediodorsal thalamus
Margalida A. Frau-Mendez et al.
BRAIN PATHOLOGY (2017)
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1 → 4-bonded polyglucose chains
Emilia A. Lubecka et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains
Mariusz Makowski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Molecular dynamics simulations of early steps in RNA-mediated conversion of prions
Erik J. Alred et al.
PROTEIN SCIENCE (2017)
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik et al.
CHEMICAL REVIEWS (2016)
Mechanisms of prion-induced neurodegeneration
Paula Saa et al.
EXPERT REVIEWS IN MOLECULAR MEDICINE (2016)
Assessing the Current State of Amber Force Field Modifications for DNA
Rodrigo Galindo-Murillo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Physics-Based Potentials for Coarse-Grained Modeling of Protein DNA Interactions
Yanping Yin 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)
The I-TASSER Suite: protein structure and function prediction
Jianyi Yang et al.
NATURE METHODS (2015)
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions
Adam Liwo et al.
JOURNAL OF MOLECULAR MODELING (2014)
Probing the N-Terminal β-Sheet Conversion in the Crystal Structure of the Human Prion Protein Bound to a Nanobody
Romany N. N. Abskharon et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
Rui Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
Romelia Salomon-Ferrer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
The prion protein M129V polymorphism Longevity and cognitive impairment among Polish centenarians
Ewa Golanska et al.
PRION (2013)
Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism
Ivana Biljan et al.
BIOCHEMICAL JOURNAL (2012)
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
Andreas W. Goetz et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Dissociation of Infectivity from Seeding Ability in Prions with Alternate Docking Mechanism
Michael B. Miller et al.
PLOS PATHOGENS (2011)
PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides
Wei Han et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
Oleg Trott et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Axonal prion protein is required for peripheral myelin maintenance
Juliane Bremer et al.
NATURE NEUROSCIENCE (2010)
I-TASSER: a unified platform for automated protein structure and function prediction
Ambrish Roy et al.
NATURE PROTOCOLS (2010)
Formation of native prions from minimal components in vitro
Nathan R. Deleault et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function
Franciszek Rakowski et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Solid-state NMR structural studies of the fibril form of a mutant mouse prion peptide PrP89-143(P101L)
KH Lim et al.
SOLID STATE NUCLEAR MAGNETIC RESONANCE (2006)
Molecular dynamics with the united-residue model of polypeptide chains.: II.: Langevin and Berendsen-Bath dynamics and tests on model α-helical systems
M Khalili et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126
K Kuwata et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
RNA molecules stimulate prion protein conversion
NR Deleault et al.
NATURE (2003)
Simulations of biomolecules: characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein
DOV Alonso et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2002)