Contrastive Learning of Coarse-Grained Force Fields

Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation

(2021) Andrew P. Latham et al.   Journal of Chemical Theory and Computation

DeepBAR: A Fast and Exact Method for Binding Free Energy Computation

(2021) Xinqiang Ding et al.   Journal of Physical Chemistry Letters

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

(2021) Stephen E. Farr et al.   Nature Communications

Unifying coarse-grained force fields for folded and disordered proteins

(2021) Andrew P. Latham et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

(2021) Giulio Tesei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

(2020) Kirill Shmilovich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems

(2020) Paraskevi Gkeka et al.   Journal of Chemical Theory and Computation

Targeted free energy estimation via learned mappings

(2020) Peter Wirnsberger et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse graining molecular dynamics with graph neural networks

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

Improving Coarse-Grained Protein Force Fields with Small-Angle X-Ray Scattering Data

(2019) Andrew P. Latham et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations

(2019) Xinqiang Ding et al.   Journal of Chemical Theory and Computation

Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

(2019) Frank Noé et al.   SCIENCE

DeePCG: Constructing coarse-grained models via deep neural networks

(2018) Linfeng Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

(2018) Linfeng Zhang et al.   PHYSICAL REVIEW LETTERS

Sequence determinants of protein phase behavior from a coarse-grained model

(2018) Gregory L. Dignon et al.   PLoS Computational Biology

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins

(2018) Hao Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models

(2017) Tobias Lemke et al.   Journal of Chemical Theory and Computation

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

(2017) Rachael A. Mansbach et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

(2016) John M. A. Grime et al.   Nature Communications

A generalized-Yvon-Born-Green method for coarse-grained modeling

(2015) J. F. Rudzinski et al.   European Physical Journal-Special Topics

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

(2015) Leonardo Darré 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

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

MagiC: Software Package for Multiscale Modeling

(2013) Alexander Mirzoev et al.   Journal of Chemical Theory and Computation

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Thermodynamic Consistency in Variable-Level Coarse Graining of Polymeric Liquids

(2012) A. J. Clark et al.   PHYSICAL REVIEW LETTERS

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

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

How Fast-Folding Proteins Fold

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

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed β-Hairpin

(2010) Wenfei Li et al.   BIOPHYSICAL JOURNAL

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

Generalized Yvon-Born-Green Theory for Molecular Systems

(2009) J. W. Mullinax et al.   PHYSICAL REVIEW LETTERS

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

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

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

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS