MolClustPy: a Python package to characterize multivalent biomolecular clusters.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37326981.
- Also identified by DOI 10.1093/bioinformatics/btad385 and PMC identifier 10290549.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become supply-limited large clusters. In stochastic simulations, such clusters display a wide range of sizes and compositions. We have developed a Python package, MolClustPy, which performs multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator); MolClustPy characterizes and visualizes the distribution of cluster sizes, molecular composition, and bonds across molecular clusters. The statistical analysis offered by MolClustPy is readily applicable to other stochastic simulation software, such as SpringSaLaD and ReaDDy. The software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide, and examples are freely available at https://molclustpy.github.io/.
Medical subject headings
- Research Design
- Software