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High-resolution Markov state models for the dynamics of Trp-cage
  miniprotein constructed over slow folding modes identified by state-free
  reversible VAMPnets

High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets

12 June 2019
Hythem Sidky
Wei Chen
Andrew L. Ferguson
ArXiv (abs)PDFHTML

Papers citing "High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets"

10 / 10 papers shown
Title
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
Tuğçe Gökdemir
Jakub Rydzewski
112
2
0
31 Dec 2024
Flow Matching for Optimal Reaction Coordinates of Biomolecular System
Flow Matching for Optimal Reaction Coordinates of Biomolecular System
Mingyuan Zhang
Zhicheng Zhang
Yong Wang
Hao Wu
101
1
0
30 Aug 2024
Reaction coordinate flows for model reduction of molecular kinetics
Reaction coordinate flows for model reduction of molecular kinetics
Hao Wu
Frank Noé
99
12
0
11 Sep 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for
  Non-Deterministic Backmapping of Cα Protein Traces
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces
Michael S. Jones
Kirill Shmilovich
Andrew L. Ferguson
DiffM
79
14
0
23 Jul 2023
Accurate Free Energy Estimations of Molecular Systems Via Flow-based
  Targeted Free Energy Perturbation
Accurate Free Energy Estimations of Molecular Systems Via Flow-based Targeted Free Energy Perturbation
Soo-Jung Lee
Amr H. Mahmoud
M. Lill
59
0
0
23 Feb 2023
Fast conformational clustering of extensive molecular dynamics
  simulation data
Fast conformational clustering of extensive molecular dynamics simulation data
Simon Hunkler
K. Diederichs
O. Kukharenko
Christine Peter
63
9
0
11 Jan 2023
GraphVAMPNet, using graph neural networks and variational approach to
  markov processes for dynamical modeling of biomolecules
GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules
Mahdi Ghorbani
Samarjeet Prasad
Jeffery B. Klauda
B. Brooks
GNN
49
32
0
12 Jan 2022
Variational embedding of protein folding simulations using gaussian
  mixture variational autoencoders
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders
Mahdi Ghorbani
Samarjeet Prasad
Jeffery B. Klauda
B. Brooks
DRL
29
17
0
27 Aug 2021
Machine Learning Force Fields
Machine Learning Force Fields
Oliver T. Unke
Stefan Chmiela
H. E. Sauceda
M. Gastegger
I. Poltavsky
Kristof T. Schütt
A. Tkatchenko
K. Müller
AI4CE
141
940
0
14 Oct 2020
Molecular Latent Space Simulators
Molecular Latent Space Simulators
Hythem Sidky
Wei Chen
Andrew L. Ferguson
AI4CE
64
34
0
01 Jul 2020
1