Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics

Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces

(2023) Jonas Köhler et al.   Journal of Chemical Theory and Computation

Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship

(2022) Jaehyeok Jin et al.   JOURNAL OF CHEMICAL PHYSICS

Deep coarse-grained potentials via relative entropy minimization

(2022) Stephan Thaler et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse graining molecular dynamics with graph neural networks

(2020) Brooke E. Husic et al.   JOURNAL OF CHEMICAL PHYSICS

A multiscale coarse-grained model of the SARS-CoV-2 virion

(2020) Alvin Yu et al.   BIOPHYSICAL JOURNAL

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

(2019) Jiang Wang et al.   ACS Central Science

Coarse-graining molecular systems by spectral matching

(2019) Feliks Nüske et al.   JOURNAL OF CHEMICAL PHYSICS

Learning Effective Molecular Models from Experimental Observables

(2018) Justin Chen et al.   Journal of Chemical Theory and Computation

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   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

Structural Basis of Membrane Bending by the N-BAR Protein Endophilin

(2012) Carsten Mim et al.   CELL

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

A Connection Between Score Matching and Denoising Autoencoders

(2011) Pascal Vincent   NEURAL COMPUTATION

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY