MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters

Abstract

AbstractSummaryLow-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become extra-large clusters. Characterizing the physical properties of these clusters is important in recent biophysical research. Due to weak interactions such clusters are highly stochastic, demonstrating a wide range of sizes and compositions. We have developed a Python package to perform multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator), characterize and visualize the distribution of cluster sizes, molecular composition, and bonds across molecular clusters and individual molecules of different types.Availability and implementationThe software is implemented in Python. A detailed Jupyter notebook is provided to enable convenient running. Code, user guide and examples are freely available athttps://molclustpy.github.io/Contactachattaraj007@gmail.com,blinov@uchc.eduSupplementary informationAvailable athttps://molclustpy.github.io/