title: ÐÐµÑÐ¾Ð´ ÑÐ¾Ð¾ÑÐ½ÐµÑÐµÐ½Ð¸Ñ ÑÐ»ÐµÐ¼ÐµÐ½ÑÐ¾Ð² Ð²ÑÐ¾ÑÐ¸ÑÐ½Ð¾Ð¹ ÑÑÑÑÐºÑÑÑÑ Ð±ÐµÐ»ÐºÐ° Ð¿Ð¾ ÑÑÐ°ÐµÐºÑÐ¾ÑÐ¸ÑÐ¼ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸ Ð¿ÑÑÐµÐ¼ Ð¿ÑÑÐ¼Ð¾Ð³Ð¾ ÑÐ°ÑÑÑÑÐ° ÑÐµÑÐºÐ¸ Ð²Ð¾Ð´Ð¾ÑÐ¾Ð´Ð½ÑÑ ÑÐ²ÑÐ·ÐµÐ¹
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¼Ð°Ð³Ð¸ÑÑÑÐ°
titleType: Subtitle
title: Method of correlating the elements of the secondary structure of a protein along the trajectories of molecular dynamics by direct calculation of the hydrogen bond grid
Creators: name: ÐÐ¾ÑÐµÐ»Ð¾Ð², Ð¡ÐµÑÐ³ÐµÐ¹
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2023
Subjects: GROMACS
DSSP
Ð²Ð¾Ð´Ð¾ÑÐ¾Ð´Ð½Ð°Ñ ÑÐ²ÑÐ·Ñ
Ð²ÑÐ¾ÑÐ¸ÑÐ½Ð°Ñ ÑÑÑÑÐºÂ­ÑÑÑÐ°
Ð±ÐµÐ»ÐºÐ¸
Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð°Ñ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ°
hydrogen bond
secondary structure
proteins
molecular dynamics

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description: The given work is devoted to the description of the process of development, optimization and application of software algorithms related to the determination of hydrogen bonds in biomacromolecules and their environment. This paper describes the principles of operation of the created algorithms for evaluating hydrogen bond networks and determining the secondary structure based on hydrogen bond templates in molecular dynamics trajectories, as well as the analysis of a number of protein structures using the developed algorithms. The developed algorithm for determining the secondary structure was applied to obtain a detailed information about the qualitative and quantitative composition of secondary structures in a protein from the molecular dynamics trajectory of randomly taken proteins. Recreated algorithm for determining hydrogen bond networks was applied to obtain qualitative and quantitative characteristics of hydrogen bonds between protein atoms, between water molecules, and between protein and water atoms from the molecular dynamics trajectory of arbitrary proteins. It is shown that the developed algorithms work faster than their counterparts, while giving identical results. The developed software algorithms can be used to study the biophysical properties of protein molecules.