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bioRxiv · 10.1101/2023.03.14.532640

MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters

Chattaraj, A.·Nalagandla, I.·Loew, L. M.·Blinov, M. L.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSSO_SCPLOWUMMARYC_SCPLOWC_ST_ABSLow-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. AO_SCPLOWVAILABILITYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWANDC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWIMPLEMENTATIONC_SCPLOWThe 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/ CO_SCPLOWONTACTC_SCPLOWachattaraj007@gmail.com, blinov@uchc.edu SO_SCPLOWUPPLEMENTARYC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWINFORMATIONC_SCPLOWAvailable at https://molclustpy.github.io/

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Chattaraj, A., Nalagandla, I., Loew, L. M., Blinov, M. L.. 2023-03-15. MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters. https://doi.org/10.1101/2023.03.14.532640

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