ArticlePLoS computational biology2023
OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.Nature structural & molecular biology · 2026Article
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 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
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- CASPULE: A computational tool to study sticker spacer polymer condensates.PLoS computational biology · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Determination of Nucleotide-Nucleotide and Nucleotide-Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations.ACS physical chemistry Au · 2026Article
- The filamentous ultrastructure of the PopZ condensate is required for its cellular function.Nature structural & molecular biology · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.Journal of chemical theory and computation · 2025Article
- CASPULE: A computational tool to study sticker spacer polymer condensates.bioRxiv : the preprint server for biology · 2025Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Protein language model identifies disordered, conserved motifs implicated in phase separation.eLife · 2025Article
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.bioRxiv : the preprint server for biology · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- Design and Characterization of DNA-Driven Condensates: Regulating Topology, Mechanical Properties, and Immunorecognition.ACS applied materials & interfaces · 2025Article
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Abstract
Biomolecular condensates are important structures in various cellular processes but are challenging to study using traditional experimental techniques. In silico simulations with residue-level coarse-grained models strike a balance between computational efficiency and chemical accuracy. They could offer valuable insights by connecting the emergent properties of these complex systems with molecular sequences. However, existing coarse-grained models often lack easy-to-follow tutorials and are implemented in software that is not optimal for condensate simulations. To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. We also provide tools that convert coarse-grained configurations to all-atom structures for atomistic simulations. We anticipate that OpenABC will significantly facilitate the adoption of in silico simulations by a broader community to investigate the structural and dynamical properties of condensates.
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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.