OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates

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 o...

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Bibliographic Details
Published in:PLoS computational biology 2023-09, Vol.19 (9), p.e1011442
Main Authors: Liu, Shuming, Wang, Cong, Latham, Andrew P, Ding, Xinqiang, Zhang, Bin
Format: Article
Language:English
Subjects:
Amino acids
Analysis
Biological systems
Biology and Life Sciences
Biomolecular Condensates
Cellular structure
Complex systems
Computer and Information Sciences
Computer Simulation
Condensates
Engineering and Technology
Graphics processing units
Molecular dynamics
Phase transitions
Physical Sciences
Proteins
Python
Research Design
Simulation
Simulation methods
Software
Software packages
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Summary: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.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1011442