DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces

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

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

Machine learned coarse-grained protein force-fields: Are we there yet?

(2023) Aleksander E.P. Durumeric et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ensuring thermodynamic consistency with invertible coarse-graining

(2023) Shriram Chennakesavalu et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics

(2023) Andreas Krämer et al.   Journal of Physical Chemistry Letters

Diffusion Models: A Comprehensive Survey of Methods and Applications

(2023) Ling Yang et al.   ACM COMPUTING SURVEYS

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

(2023) Marloes Arts et al.   Journal of Chemical Theory and Computation

Machine learning coarse-grained potentials of protein thermodynamics

(2023) Maciej Majewski et al.   Nature Communications

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

(2022) Cheng Tan et al.   PLoS Computational Biology

From data to noise to data for mixing physics across temperatures with generative artificial intelligence

(2022) Yihang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contrastive Learning of Coarse-Grained Force Fields

(2022) Xinqiang Ding et al.   Journal of Chemical Theory and Computation

Orbital Mixer: Using Atomic Orbital Features for Basis-Dependent Prediction of Molecular Wavefunctions

(2022) Kirill Shmilovich et al.   Journal of Chemical Theory and Computation

Benchmarking coarse-grained models of organic semiconductors via deep backmapping

(2022) Marc Stieffenhofer et al.   Frontiers in Chemistry

Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution

(2022) Kirill Shmilovich et al.   Journal of Physical Chemistry A

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

(2021) Wei Lu et al.   PLoS Computational Biology

Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability

(2021) Marc Stieffenhofer et al.   APL Materials

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

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

SidechainNet : An all‐atom protein structure dataset for machine learning

(2021) Jonathan Edward King et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Backmapping coarse-grained macromolecules: An efficient and versatile machine learning approach

(2020) Wei Li et al.   JOURNAL OF CHEMICAL PHYSICS

Generative adversarial networks

(2020) Ian Goodfellow et al.   COMMUNICATIONS OF THE ACM

Coarse graining molecular dynamics with graph neural networks

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

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

(2019) Jiang Wang et al.   ACS Central Science

ProteinNet: a standardized data set for machine learning of protein structure

(2019) Mohammed AlQuraishi   BMC BIOINFORMATICS

1CPN: A coarse-grained multi-scale model of chromatin

(2019) Joshua Lequieu et al.   JOURNAL OF CHEMICAL PHYSICS

High-Resolution Markov State Models for the Dynamics of Trp-Cage Miniprotein Constructed Over Slow Folding Modes Identified by State-Free Reversible VAMPnets

(2019) Hythem Sidky et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes

(2019) Jared M Sagendorf et al.   NUCLEIC ACIDS RESEARCH

Coarse-graining auto-encoders for molecular dynamics

(2019) Wujie Wang et al.   npj Computational Materials

DeePCG: Constructing coarse-grained models via deep neural networks

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

SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol

(2018) Sangjae Seo et al.   Journal of Chemical Theory and Computation

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

(2018) John M. Jumper et al.   PLoS Computational Biology

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

(2017) Joerg Schaarschmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SIRAH tools: mapping, backmapping and visualization of coarse-grained models

(2016) Matías R. Machado et al.   BIOINFORMATICS

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

CG2AA: backmapping protein coarse-grained structures

(2015) Leandro E. Lombardi et al.   BIOINFORMATICS

Coarse-Graining Methods for Computational Biology

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

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Critical assessment of methods of protein structure prediction (CASP) - round x

(2013) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Multiscale molecular dynamics simulations of micelles: coarse-grain for self-assembly and atomic resolution for finer details

(2012) Pilar Brocos et al.   Soft Matter

Multiscale modeling of soft matter: scaling of dynamics

(2011) Dominik Fritz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Fast-Folding Proteins Fold

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

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

(2011) Axel Drefahl   Journal of Cheminformatics

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification

(2010) Wei Han et al.   Journal of Chemical Theory and Computation

Reconstruction of atomistic details from coarse-grained structures

(2010) Andrzej J. Rzepiela et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome

(2010) Joanna Trylska   JOURNAL OF PHYSICS-CONDENSED MATTER

Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear1H−15N NMR Spectroscopy

(2010) Alexandre Esadze et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

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

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

(2008) Kathryn A. Scott et al.   STRUCTURE

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

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY