ArticleNature communications2022
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 140 citations in OpenAlex.
- Article
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- Fast-Forward: Automatic Assignment and Assessment of Bonded Parameters for the Martini Force Field.Journal of chemical information and modeling · 2026Article
- Analytical coarse grained potential parameterization by reinforcement learning for anisotropic cellulose.Journal of molecular modeling · 2026Article
- The molecular basis of mitochondrial crista formation by the MIC10 complex.Science advances · 2026Article
- PolyRapid: automated high-throughput screening of polymers using a computational workflow.Soft matter · 2026Article
- Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026Article
- Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS.The journal of physical chemistry. B · 2026Article
- High-Efficiency Asymmetric Spin Transport Enabled by Nanocolumn Molecular Semiconductors.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Assessing the Martini Force Field for Modeling Polyolefin Nanoplastics near Lipid Membranes.The journal of physical chemistry. B · 2026Article
- MolPy: A Large Language Model-Friendly Toolkit for Reactive Topology Editing in Polymer Simulations.Journal of chemical information and modeling · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- De novo design of peptides localizing at the interface of biomolecular condensates.Nature communications · 2026Article
- Encapsulation of colistin using hyaluronic acid and PVA-PSS polymeric nanocarriers for enhanced drug delivery: a molecular dynamics simulation study.Scientific reports · 2026Article
- Condensates as Conformation Editors of Disordered Client Proteins.Journal of the American Chemical Society · 2026Article
- Folded domains impose structural heterogeneity and attenuated dynamics in biomolecular condensates.Nature communications · 2026Article
- Ultrasound-responsive liposomes: A mechanistic framework to decode the effects of acoustic parameters.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Atomic-level architecture and assembly mechanism of high-order structures of RIPK1 fibril revealed by integrated structural biology.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle.
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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.