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bioRxiv · 10.1101/2024.02.17.580696

Random sampling of ligand arrangements on a one-dimensional lattice

Mohanta, D.·Dvirnas, A.·Ambjörnsson, T.
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Abstract

We introduce a transfer-matrix-based sequential sampling scheme for generating random samples of ligand arrangements on one-dimensional templates. The number of ligand types is arbitrary, the binding constants can have positional dependence, and cooperativity parameters are included. From the random arrangements, any (linear or non-linear) observable can be calculated using sample averaging. We provide a publically available software with a computational time that scales linearly with the lattice size. As an example application, we study the competitive binding of three ligand types (the sequence-specific binder netropsin, YOYO-1 and ethidium bromide) to a DNA molecule.

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Mohanta, D., Dvirnas, A., Ambjörnsson, T.. 2024-02-21. Random sampling of ligand arrangements on a one-dimensional lattice. https://doi.org/10.1101/2024.02.17.580696

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