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。Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods
Hao Tian et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)
ivis Dimensionality Reduction Framework for Biomacromolecular Simulations
Hao Tian et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain
Hao Tian et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2020)
Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach
Zilin Song et al.
COMMUNICATIONS CHEMISTRY (2020)
The single-cell transcriptional landscape of mammalian organogenesis
Junyue Cao et al.
NATURE (2019)
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis
Hongyu Zhou et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution
Jonathan S. Packer et al.
SCIENCE (2019)
UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts
Alex Diaz-Papkovich et al.
PLOS GENETICS (2019)
Dimensionality reduction for visualizing single-cell data using UMAP
Etienne Becht et al.
NATURE BIOTECHNOLOGY (2019)
Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase
Feng Wang et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2019)
Using Dimensionality Reduction to Analyze Protein Trajectories
Gareth A. Tribello et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2019)
Markov State Models: From an Art to a Science
Brooke E. Husic et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)
t-Distributed Stochastic Neighbor Embedding Method with the Least Information Loss for Macromolecular Simulations
Hongyu Zhou et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations
Gerard Martinez-Rosell et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables
Mohammad M. Sultan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
The folding mechanism and key metastable state identification of the PrP127-147 monomer studied by molecular dynamics simulations and Markov state model analysis
Shuangyan Zhou et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information
Zahra Shamsi et al.
SCIENTIFIC REPORTS (2017)
MSMBuilder: Statistical Models for Biomolecular Dynamics
Matthew P. Harrigan et al.
BIOPHYSICAL JOURNAL (2017)
Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Diwakar Shukla et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
Peter Eastman et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
Christian R. Schwantes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Evaluation of Dimensionality-Reduction Methods from Peptide Folding-Unfolding Simulations
Mojie Duan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Signaling mechanisms of LOV domains: new insights from molecular dynamics studies
Peter L. Freddolino et al.
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES (2013)
Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function
Ulf Hensen et al.
PLOS ONE (2012)
Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach
Andrew L. Ferguson et al.
CHEMICAL PHYSICS LETTERS (2011)
Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions
Yusuke Naritomi et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
High-resolution mapping of protein sequence-function relationships
Douglas M. Fowler et al.
NATURE METHODS (2010)
Everything you wanted to know about Markov State Models but were afraid to ask
Vijay S. Pande et al.
METHODS (2010)
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
Hernan Stamati et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Long-timescale molecular dynamics simulations of protein structure and function
John L. Klepeis et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
Progress and challenges in the automated construction of Markov state models for full protein systems
Gregory R. Bowman et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
CHARMM: The Biomolecular Simulation Program
B. R. Brooks et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
TRANSITION PATH THEORY FOR MARKOV JUMP PROCESSES
Philipp Metzner et al.
MULTISCALE MODELING & SIMULATION (2009)
Mechanism-based tuning of a LOV domain photoreceptor
Brian D. Zoltowski et al.
NATURE CHEMICAL BIOLOGY (2009)
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Light activation of the LOV protein Vivid generates a rapidly exchanging dimer
Brian D. Zoltowski et al.
BIOCHEMISTRY (2008)
Algorithmic dimensionality reduction for molecular structure analysis
W. Michael Brown et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Quantitative assessment of relationship between sequence similarity and function similarity
Trupti Joshi et al.
BMC GENOMICS (2007)
Conformational switching in the fungal light sensor vivid
Brian D. Zoltowski et al.
SCIENCE (2007)
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
Payel Das et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Towards a theory of transition paths
Weinan E et al.
JOURNAL OF STATISTICAL PHYSICS (2006)
Molecular dynamics and protein function
M Karplus et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Describing protein folding kinetics by molecular dynamics simulations.: 2.: Example applications to alanine dipeptide and β-hairpin peptide
WC Swope et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
The Protein Data Bank
HM Berman et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2002)
Molecular dynamics simulations
T Hansson et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)
Nonlinear dimensionality reduction by locally linear embedding
ST Roweis et al.
SCIENCE (2000)
分享论文
