ArticleThe journal of physical chemistry. B2023
OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining.
Article in The journal of physical chemistry. B, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Subdomains of endophilin can drive membrane remodeling and facilitate controlled membrane scission.Biophysical journal · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.Journal of the American Chemical Society · 2026Article
- On the mechanism of ezrin activation.Biophysical journal · 2026Article
- NNP/CG-MM: Embedding of All-Atom Neural Network Potentials into a Coarse-Grained Molecular Mechanics Environment.Journal of chemical theory and computation · 2026Article
- Membrane remodeling by the collective action of caveolin-1.Nature communications · 2026Article
- Collective fluctuations underlying nanobody inhibitory activity targetingbioRxiv : the preprint server for biology · 2026Article
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- The LOK C-terminus is an IBAR-like domain that facilitates membrane binding and ezrin colocalization.Biophysical journal · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.bioRxiv : the preprint server for biology · 2026Article
- Active subspace learning for coarse-grained molecular dynamics.The Journal of chemical physics · 2026Article
- Lattice instability drives formation of protofilament clusters at the microtubule plus-end tips.Biophysical journal · 2026Article
- Subdomains of Endophilin-NBAR Can Synergistically Drive Membrane Remodeling and Facilitate Controlled Membrane Scission.bioRxiv : the preprint server for biology · 2026Article
- On the curvature and relaxation of microtubule plus-end tips.Biophysical journal · 2026Article
- Active subspace learning for coarse-grained molecular dynamics.bioRxiv : the preprint server for biology · 2025Article
- On the Mechanism of Ezrin Activation.bioRxiv : the preprint server for biology · 2025Article
- Bottom-up Coarse-Grained Models of Asymmetric Membranes.The journal of physical chemistry. B · 2025Article
- Membrane Remodeling by the Collective Action of Caveolin-1.bioRxiv : the preprint server for biology · 2025Article
- MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion.Journal of chemical theory and computation · 2025Article
- A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes.Journal of chemical theory and computation · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The "bottom-up" approach to coarse-graining, for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes, is an important approach in computational chemistry, biophysics, and materials science. As one example, the Multiscale Coarse-Graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure, such as MS-CG modeling, is particularly valuable. Here, we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (EDCG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS, and NAMD. OpenMSCG is modularized in the Python programming framework, which allows users to create and customize modeling "recipes" for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.