In:
PLOS Computational Biology, Public Library of Science (PLoS), Vol. 19, No. 9 ( 2023-9-11), p. e1011442-
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.
Type of Medium:
Online Resource
ISSN:
1553-7358
DOI:
10.1371/journal.pcbi.1011442
DOI:
10.1371/journal.pcbi.1011442.g001
DOI:
10.1371/journal.pcbi.1011442.g002
DOI:
10.1371/journal.pcbi.1011442.g003
DOI:
10.1371/journal.pcbi.1011442.g004
DOI:
10.1371/journal.pcbi.1011442.g005
DOI:
10.1371/journal.pcbi.1011442.g006
DOI:
10.1371/journal.pcbi.1011442.s001
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2023
detail.hit.zdb_id:
2193340-6
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