ArticleNature communications2024
CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Development of a clinically viable MRGPRX4 inverse agonist for cholestatic itch treatment.Nature chemical biology · 2026Article
- Dual pKa Lipid Nanoparticles for Lung-tropic mRNA Delivery and pH-Programmed Endosomal Escape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Atomic structure and plasticity of the CTX-MthK complex investigated by cryo-EM, NMR, and MD simulations.Nature communications · 2026Article
- Skin Barrier Modulation by Oleyl-Based Co-Formulants: Mechanistic Insights from Molecular Simulations.ACS omega · 2026Article
- Mutant-Selective Binding ofInternational journal of molecular sciences · 2026Article
- CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field Compatibility and Robust Dense-Phase Relaxation.Journal of chemical information and modeling · 2026Article
- Dihydroartemisinin Suppresses Hepatocellular Carcinoma Progression by Acting on KIF11 with PI3K/Akt Modulation.Cancers · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Molecular Interactions of Fluoroquinolone Antibiotics with Lipid Membranes.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- A two-step screen identifies a small molecule that disrupts membrane voltage and is effective against growing and persister gram-negative bacteria.Microbiology spectrum · 2026Article
- Barriers to the Pharmacologic Rescue of W1282X CFTR.Biochemistry · 2026Article
- Conformation Driven Enhancement of Neurolysin Activity in Presence of a Small Molecule Activator.bioRxiv : the preprint server for biology · 2026Article
- Effect of Graphene Oxide Particle Size on the Enzymatic Synthesis of Polyaniline Films.Micromachines · 2025Article
- Minimalistic Peptide Nanocarriers for Multiple Cancer Drugs.ACS applied bio materials · 2025Article
- A unique gating mechanism revealed by the cryo-EM structure of monomeric ATP9A flippase.The Journal of biological chemistry · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.Nature communications · 2025Article
- Transferable Neural Network Potentials and Condensed Phase Properties.Journal of chemical information and modeling · 2025Article
- Retargeting Gram-Positive-Only Adarotene-Derived Antibacterials to Broad-Spectrum Antibiotics.Antibiotics (Basel, Switzerland) · 2025Article
- Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.bioRxiv : the preprint server for biology · 2025Article
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4 authors.
Funding
Abstract
Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. In this work, we demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to study complex interactions between small molecules, biomacromolecules, polymers, and nanomaterials.
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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.