Computer simulation of conformational motion of protein molecules using functionally specified models

Abstract

The article considers the problem of computer modeling of biological structures using functionally specified objects. Visualization is necessary for a researcher to understand the space and geometry of the object being studied. The dynamics of biological structures complicate the task. An example of a complex dynamic structure is the problem of protein folding. Efficient computational models are required to study the folding process. The aim of the work is to develop a reliable method for modeling molecular dynamics based on functionally specified objects. A method for modeling the conformational motion of protein molecules using functionally specified models is presented. The relationship between the structural organization of a protein and its functional activity, which manifests itself at the moments of protein transition from one conformation to another, is investigated. A mathematical model of the motion of protein molecules and an algorithm for conformational motion are described. An interactive modeling system is proposed based on the functional assignment of models. The test results showing the operability of the proposed model are shown. Based on the proposed method, new opportunities are opening up for research in the field of protein folding and the development of new protein structures. Protein models are also relevant for the development of self-twisting modular robots that can perform a specific task.