title: ÐÑÑÐ»ÐµÐ´Ð¾Ð²Ð°Ð½Ð¸Ðµ Ð¼ÐµÑÐ¾Ð´Ð¾Ð² Ð³Ð»Ð¾Ð±Ð°Ð»ÑÐ½Ð¾Ð¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ Ð² Ð¿ÑÐ¸Ð¼ÐµÐ½ÐµÐ½Ð¸Ð¸ Ðº Ð·Ð°Ð´Ð°ÑÐµ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·Ð¸ Ð¾ÑÐ³Ð°Ð½Ð¸ÑÐµÑÐºÐ¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»
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: Investigation of global optimization methods as applied to the problem of computing the binding energy of organic molecules
Creators: name: Ð¢ÐµÐ¼Ð¸ÑÐ³Ð°Ð»Ð¸ÐµÐ², Ð Ð°ÑÐ°ÑÐ»Ñ
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: ÐÐ°ÑÐµÐ¼Ð°ÑÐ¸ÑÐµÑÐºÐ¸Ð¹ Ð°Ð½Ð°Ð»Ð¸Ð·
Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½ÑÐ¹ Ð´Ð¾ÐºÐ¸Ð½Ð³
Ð¾ÑÐµÐ½ÐºÐ° ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÐºÐ¾Ð¼Ð¿Ð»ÐµÐºÑÐ° Ð¼Ð¾Ð»ÐµÐºÑÐ»
Ð³Ð»Ð¾Ð±Ð°Ð»ÑÐ½Ð°Ñ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ
Ð»Ð¾ÐºÐ°Ð»ÑÐ½Ð°Ñ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ
Ð³ÑÐ°Ð´Ð¸ÐµÐ½Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ
Ð¼ÐµÑÐ¾Ð´ ÐÐ¾Ð½ÑÐµ-ÐÐ°ÑÐ»Ð¾
ÑÑÑÑ Ð¼ÐµÑÐ½Ð°Ñ ÑÐµÑÐºÐ°
Ð¿Ð¾Ð´Ð³Ð¾ÑÐ¾Ð²ÐºÐ° Ð¼Ð¾Ð»ÐµÐºÑÐ»Ñ
Ð²Ð¾ÑÑÑÐ°Ð½Ð¾Ð²Ð»ÐµÐ½Ð¸Ðµ Ð²Ð¾Ð´Ð¾ÑÐ¾Ð´Ð¾Ð²
Ð¿ÑÐ¾ÑÐ¾Ð½Ð¸ÑÐ¾Ð²Ð°Ð½Ð¸Ðµ
molecular docking
energy estimation of a complex of molecules
global optimization
local optimization
binding energy gradient
Monte-Carlo method
three-dimensional grid
preparation of a molecule
hydrogen reduction
protonation

description: ÐÐ°Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° ÑÐµÐ°Ð»Ð¸Ð·Ð°ÑÐ¸Ð¸ ÑÐ¼Ð¿Ð¸ÑÐ¸ÑÐµÑÐºÐ¾Ð¹ Ð¾ÑÐµÐ½Ð¾ÑÐ½Ð¾Ð¹ ÑÑÐ½ÐºÑÐ¸Ð¸ Vinardo ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð»Ð¸Ð³Ð°Ð½Ð´Ð° Ñ Ð±ÐµÐ»ÐºÐ¾Ð¼ Ð¸ Ð¿ÑÐ¸Ð¼ÐµÐ½ÐµÐ½Ð¸Ñ ÑÑÐ¾Ð¹ Ð¾ÑÐµÐ½ÐºÐ¸ Ð² Ð·Ð°Ð´Ð°ÑÐµ Ð³Ð»Ð¾Ð±Ð°Ð»ÑÐ½Ð¾Ð¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ÐºÐ¾Ð½ÑÐ¸Ð³ÑÑÐ°ÑÐ¸Ð¸ Ð»Ð¸Ð³Ð°Ð½Ð´Ð° Ð² Ð±ÐµÐ»ÐºÐµ Ñ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸ÐµÐ¼ Ð¼ÐµÑÐ¾Ð´Ð° Ð»Ð¾ÐºÐ°Ð»ÑÐ½Ð¾Ð¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ BFGS Ð¸ Ð¼ÐµÑÐ¾Ð´Ð° Ð³Ð»Ð¾Ð±Ð°Ð»ÑÐ½Ð¾Ð¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ILS. Ð ÐµÐ·ÑÐ»ÑÑÐ¸ÑÑÑÑÐ¸Ðµ Ð·Ð½Ð°ÑÐµÐ½Ð¸Ñ ÑÐ½ÐµÑÐ³Ð¸Ð¹ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ, Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½ÑÐµ Ð¿ÑÐ¸ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ Ð¿Ð¾Ð»Ð¾Ð¶ÐµÐ½Ð¸Ñ Ð»Ð¸Ð³Ð°Ð½Ð´Ð° Ð² Ð±ÐµÐ»ÐºÐµ Ð°ÐºÑÑÐ°Ð»ÑÐ½Ñ Ð² ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐºÐ°Ñ Ð»ÐµÐºÐ°ÑÑÑÐ²ÐµÐ½Ð½ÑÑ ÑÐ¾ÐµÐ´Ð¸Ð½ÐµÐ½Ð¸Ð¹. ÐÑÐ» ÑÐµÐ°Ð»Ð¸Ð·Ð¾Ð²Ð°Ð½ Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ð½ÑÐ¹ Ð¿Ð°ÐºÐµÑ, Ð¾ÑÑÑÐµÑÑÐ²Ð»ÑÐµÐ¼ÑÐ¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ñ Ð¿Ð¾Ð»Ð¾Ð¶ÐµÐ½Ð¸Ñ Ð»Ð¸Ð³Ð°Ð½Ð´Ð° Ð² Ð¼Ð¾Ð»ÐµÐºÑÐ»Ðµ Ð±ÐµÐ»ÐºÐ°. ÐÑÐ» ÑÐµÐ°Ð»Ð¸Ð·Ð¾Ð²Ð°Ð½ Ð¸ Ð¿ÑÐ¾ÑÐµÑÑÐ¸ÑÐ¾Ð²Ð°Ð½ Ð¼ÐµÑÐ¾Ð´ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ Ð³ÑÐ°Ð´Ð¸ÐµÐ½ÑÐ° Ð¾ÑÐµÐ½ÐºÐ¸ ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Ð»Ð¸Ð³Ð°Ð½Ð´Ð° Ð¸ Ð±ÐµÐ»ÐºÐ° Ñ Ð¿ÑÐµÐ´Ð²Ð°ÑÐ¸ÑÐµÐ»ÑÐ½ÑÐ¼ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸ÐµÐ¼ ÑÐ¼Ð¿Ð¸ÑÐ¸ÑÐµÑÐºÐ¾Ð¹ ÑÑÐ½ÐºÑÐ¸Ð¸ Ð½Ð° ÑÑÑÑÐ¼ÐµÑÐ½Ð¾Ð¹ ÑÐµÑÐºÐµ Ð¸ Ð°Ð»Ð³Ð¾ÑÐ¸ÑÐ¼ Ð³Ð»Ð¾Ð±Ð°Ð»ÑÐ½Ð¾Ð¹ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ILS Ð½Ð° Ð¾ÑÐ½Ð¾Ð²Ðµ Ð¼ÐµÑÐ¾Ð´Ð° ÑÐ»ÑÑÐ°Ð¹Ð½Ð¾Ð³Ð¾ Ð¿Ð¾Ð¸ÑÐºÐ° ÐÐ¾Ð½ÑÐµ-ÐÐ°ÑÐ»Ð¾. ÐÐ¾ÑÐ»Ðµ ÑÐµÐ°Ð»Ð¸Ð·Ð°ÑÐ¸Ð¸ Ð¸ ÑÐµÑÑÐ¸ÑÐ¾Ð²Ð°Ð½Ð¸Ñ Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ð½Ð¾Ð³Ð¾ Ð¿Ð°ÐºÐµÑÐ° Ð±ÑÐ» Ð¿ÑÐ¾Ð²ÐµÐ´ÑÐ½ ÑÑÐ°Ð²Ð½Ð¸ÑÐµÐ»ÑÐ½ÑÐ¹ Ð°Ð½Ð°Ð»Ð¸Ð· Ð±ÑÑÑÑÐ¾Ð´ÐµÐ¹ÑÑÐ²Ð¸Ñ Ð¸ ÑÐ¾ÑÐ½Ð¾ÑÑÐ¸ Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½Ð¾Ð¹ Ð¾ÑÐµÐ½ÐºÐ¸ ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐ°Ð½Ð½Ð¾Ð¹ ÑÐµÐ°Ð»Ð¸Ð·Ð°ÑÐ¸Ð¸ Ð¾Ð¿ÑÐ¸Ð¼Ð¸Ð·Ð°ÑÐ¸Ð¸ ÑÐ½ÐµÑÐ³Ð¸Ð¸ ÑÐ²ÑÐ·ÑÐ²Ð°Ð½Ð¸Ñ Vinardo Ñ Ð°Ð½Ð°Ð»Ð¾Ð³Ð¸ÑÐ½Ð¾Ð¹ ÑÐµÐ°Ð»Ð¸Ð·Ð°ÑÐ¸ÐµÐ¹ Ð² Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ð½Ð¾Ð¼ Ð¿Ð°ÐºÐµÑÐµ smina Ð½Ð° Ð¿Ð°ÑÐ°Ñ Ð»Ð¸Ð³Ð°Ð½Ð´-Ð±ÐµÐ»Ð¾Ðº Ð¸Ð· Ð½Ð°Ð±Ð¾ÑÐ° Ð´Ð°Ð½Ð½ÑÑ DUD-E.
description: This work is devoted to the implementation of the Vinardo empirical estimation function of the binding energy of a ligand to a protein and the application of this estimate in the problem of global optimization of the ligand configuration in a protein using the BFGS local optimization method and the ILS global optimization method. The resulting values of binding energies obtained by optimizing the position of the ligand in the protein are relevant in the development of drug compounds. A software package was implemented that optimizes the position of the ligand in the protein molecule. A method for calculating the gradient of ligand and protein binding energy estimation with preliminary calculation of the empirical function on a three-dimensional grid, a ILS global optimization algorithm based on the Monte Carlo random search method was implemented and tested. After the implementation and testing of the software package, a comparative analysis of the speed and accuracy of the obtained estimate of the developed implementation of Vinardo binding energy optimization with a similar implementation in the smina software package was carried out on ligand-protein pairs from the DUD-E data set.