Using MTBindingSim as a tool for experimental planning and interpretation.

MTBindingSim is a program that enables users to simulate experiments in which proteins or other ligands (e.g., drugs) bind to microtubules or other polymers under various binding models. The purpose of MTBindingSim is to help researchers and students gain an intuitive understanding of binding behavior and design experiments to distinguish between different binding mechanisms. MTBindingSim is open-source, freely available software and can be found at bindingtutor.org/mtbindingsim. This chapter first describes the capabilities of MTBindingSim, including the experimental designs and protein-binding models that it simulates, and then discusses two examples in which MTBindingSim is utilized in an experimental context. In the first, MTBindingSim is used to investigate potential explanations for unusual behavior observed in the binding of the neuronal protein Tau to microtubules, demonstrating that some potential explanations are incompatible with the experimental data. In the second example, MTBindingSim is used to design experiments to examine the question of whether the plus-end tracking protein EB1 binds preferentially to the microtubule seam.