Скачать или смотреть Pawel Rubach's talk at MACSMIN 2025,

Speaker. Paweł Rubach (Warsaw School of Economics, Poland).

Title. Identification of Non-trivial Topologies in Biopolymers.

Abstract. The topology of biopolymers plays a crucial role in their function and properties. In particular, the effect of knots, slipknots, and links in linear polymers was studied in designed compounds and proteins. The inclusion of branching points showed the existence of the theta-curve topology, lasso motif or cysteine knots, where the depth of the piercing affects the properties of the polymer. To efficiently identify these non-trivial topologies we created the Topoly Python package. Topoly enables the distinguishing of knots, slipknots, links, and spatial graphs through the calculation of different polynomials. It also enables one to create the minimal spanning surface on a given loop e.g., to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including CIF and PDB. The extensive documentation along with test cases and the simplicity of the Python programming language makes it a very simple to use, yet powerful tool, suitable even for inexperienced users.