Study of model problem of structural bioinformatics

The paper is devoted to the study of methods for solving problems of structural bioinformatics on the example of solving a model problem of graphs layout on a plane. The paper considers an "energy" approach to solving this type of problems, based on the use of continuous optimization methods, the purpose of which is to find a configuration with a minimum energy. The paper formulates a model problem of graph layout, describes the structure of graphs to be processed, and defines an objective function that simulates the internal energy of graph layout. Several popular optimization methods are described, including a genetic algorithm and a differential evolution algorithm. Parallel variations of these two algorithms are considered. Implementation of a software system for automatic testing of a user-defined algorithm for solving model folding problems with support for parallel computing, web interface and visualization of computations is described. The work was carried out with the financial support of the Russian Foundation for Basic Research (Grant No. 20-07-01053 A).