Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics
Authors
Keywords
-
Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 148, Issue 24, Pages 241703
Publisher
AIP Publishing
Online
2018-03-15
DOI
10.1063/1.5011399
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- VAMPnets for deep learning of molecular kinetics
- (2018) Andreas Mardt et al. Nature Communications
- Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations
- (2017) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias
- (2017) Feliks Nüske et al. JOURNAL OF CHEMICAL PHYSICS
- Deep learning for computational chemistry
- (2017) Garrett B. Goh et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations
- (2017) Rodrigo Casasnovas et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
- (2017) Nuria Plattner et al. Nature Chemistry
- Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces
- (2017) Elia Schneider et al. PHYSICAL REVIEW LETTERS
- Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
- (2017) Fabian Paul et al. Nature Communications
- Quantum-chemical insights from deep tensor neural networks
- (2017) Kristof T. Schütt et al. Nature Communications
- How and when does an anticancer drug leave its binding site?
- (2017) Pratyush Tiwary et al. Science Advances
- Variational tensor approach for approximating the rare-event kinetics of macromolecular systems
- (2016) Feliks Nüske et al. JOURNAL OF CHEMICAL PHYSICS
- HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
- (2016) S. Doerr et al. Journal of Chemical Theory and Computation
- Mastering the game of Go with deep neural networks and tree search
- (2016) David Silver et al. NATURE
- Auto-encoder based dimensionality reduction
- (2016) Yasi Wang et al. NEUROCOMPUTING
- Multiensemble Markov models of molecular thermodynamics and kinetics
- (2016) Hao Wu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Discovering governing equations from data by sparse identification of nonlinear dynamical systems
- (2016) Steven L. Brunton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Topological obstructions in the way of data-driven collective variables
- (2015) Behrooz Hashemian et al. JOURNAL OF CHEMICAL PHYSICS
- Variational cross-validation of slow dynamical modes in molecular kinetics
- (2015) Robert T. McGibbon et al. JOURNAL OF CHEMICAL PHYSICS
- Modeling Molecular Kinetics with tICA and the Kernel Trick
- (2015) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation
- (2015) Frank Noé et al. Journal of Chemical Theory and Computation
- PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
- (2015) Martin K. Scherer et al. Journal of Chemical Theory and Computation
- A Data–Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition
- (2015) Matthew O. Williams et al. JOURNAL OF NONLINEAR SCIENCE
- Deep learning
- (2015) Yann LeCun et al. NATURE
- Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
- (2015) Nuria Plattner et al. Nature Communications
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
- (2014) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Variational Approach to Molecular Kinetics
- (2014) Feliks Nüske et al. Journal of Chemical Theory and Computation
- Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
- (2014) Edina Rosta et al. Journal of Chemical Theory and Computation
- Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics
- (2014) Jordane Preto et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Spectral Rate Theory for Two-State Kinetics
- (2014) Jan-Hendrik Prinz et al. Physical Review X
- xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States
- (2014) Antonia S. J. S. Mey et al. Physical Review X
- Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
- (2013) Mary A. Rohrdanz et al. Annual Review of Physical Chemistry
- GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
- (2013) Sander Pronk et al. BIOINFORMATICS
- Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
- (2013) Behrooz Hashemian et al. JOURNAL OF CHEMICAL PHYSICS
- Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling
- (2013) Zheng Yi et al. JOURNAL OF CHEMICAL PHYSICS
- Identification of slow molecular order parameters for Markov model construction
- (2013) Guillermo Pérez-Hernández et al. JOURNAL OF CHEMICAL PHYSICS
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
- (2013) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems
- (2013) Frank Noé et al. MULTISCALE MODELING & SIMULATION
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
- (2013) Kai J. Kohlhoff et al. Nature Chemistry
- Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning
- (2012) Matthias Rupp et al. PHYSICAL REVIEW LETTERS
- Kinetic characterization of the critical step in HIV-1 protease maturation
- (2012) S. K. Sadiq et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Determination of reaction coordinates via locally scaled diffusion map
- (2011) Mary A. Rohrdanz et al. JOURNAL OF CHEMICAL PHYSICS
- Markov models of molecular kinetics: Generation and validation
- (2011) Jan-Hendrik Prinz et al. JOURNAL OF CHEMICAL PHYSICS
- Simplifying the representation of complex free-energy landscapes using sketch-map
- (2011) Michele Ceriotti et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
- (2011) I. Buch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- How Fast-Folding Proteins Fold
- (2011) K. Lindorff-Larsen et al. SCIENCE
- A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
- (2011) Daniel-Adriano Silva et al. PLoS Computational Biology
- High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
- (2010) I. Buch et al. Journal of Chemical Information and Modeling
- Systematic determination of order parameters for chain dynamics using diffusion maps
- (2010) A. L. Ferguson et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Atomic-Level Characterization of the Structural Dynamics of Proteins
- (2010) D. E. Shaw et al. SCIENCE
- Progress and challenges in the automated construction of Markov state models for full protein systems
- (2009) Gregory R. Bowman et al. JOURNAL OF CHEMICAL PHYSICS
- ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
- (2009) M. J. Harvey et al. Journal of Chemical Theory and Computation
- Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
- (2009) Frank Noé et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
- (2009) Hernán Stamati et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Algorithmic dimensionality reduction for molecular structure analysis
- (2008) W. Michael Brown et al. JOURNAL OF CHEMICAL PHYSICS
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now