ArticleJournal of chemical theory and computation2021
CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations.
Article in Journal of chemical theory and computation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed, 152 citations in OpenAlex.
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- Structural basis of outer membrane biogenesis by the TamAB translocase.Nature communications · 2026Article
- Human class B1 GPCR modulation by plasma membrane lipids.Communications biology · 2026Article
- Structural snapshots of Pseudomonas aeruginosa LptBNature communications · 2025Article
- Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria.Nature communications · 2025Article
- Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane.Communications biology · 2025Article
- Mechanistic basis of antimicrobial resistance mediated by the phosphoethanolamine transferase MCR-1.Nature communications · 2025Article
- Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex.Nature communications · 2025Article
- CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function.Cell research · 2025Article
- TS2CG as a Membrane Builder.Journal of chemical theory and computation · 2025Article
14 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well-equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of 11 system configurations of varying size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.
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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.