Design of proteins by parallel tempering in the sequence space

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F25%3A43933594" target="_blank" >RIV/60461373:22330/25:43933594 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.doi.org/10.1002/pro.70246" target="_blank" >https://www.doi.org/10.1002/pro.70246</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/pro.70246" target="_blank" >10.1002/pro.70246</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Design of proteins by parallel tempering in the sequence space

Popis výsledku v původním jazyce

Computational design of new proteins is often performed by optimizing the amino acid sequence. This sequence is characterized by an energy (lower energy means better propensity to form the desired 3D structure) that is sampled and minimized. Here, we use the parallel tempering algorithm to accelerate this task. ESMfold was used to predict the structures of the sampled proteins and calculate energy. Starting from random amino acid sequences, each sequence was sampled using the Monte Carlo method at one of a series of temperatures, and these replicas were being exchanged by the parallel tempering method. A series of 100 or 200 residue proteins was designed to maximize confidence in structure prediction and globularity and minimize surface hydrophobic residues. We show that parallel tempering is a viable alternative to Monte Carlo sampling without replica exchanges and simulated annealing or related energy-based protein design methods, especially in the situation where a continuous flow of designed sequences is desired. © 2025 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

Název v anglickém jazyce

Design of proteins by parallel tempering in the sequence space

Popis výsledku anglicky

Computational design of new proteins is often performed by optimizing the amino acid sequence. This sequence is characterized by an energy (lower energy means better propensity to form the desired 3D structure) that is sampled and minimized. Here, we use the parallel tempering algorithm to accelerate this task. ESMfold was used to predict the structures of the sampled proteins and calculate energy. Starting from random amino acid sequences, each sequence was sampled using the Monte Carlo method at one of a series of temperatures, and these replicas were being exchanged by the parallel tempering method. A series of 100 or 200 residue proteins was designed to maximize confidence in structure prediction and globularity and minimize surface hydrophobic residues. We show that parallel tempering is a viable alternative to Monte Carlo sampling without replica exchanges and simulated annealing or related energy-based protein design methods, especially in the situation where a continuous flow of designed sequences is desired. © 2025 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2025

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

PROTEIN SCIENCE

ISSN

0961-8368

e-ISSN

1469-896X

Svazek periodika

34

Číslo periodika v rámci svazku

10

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

10

Strana od-do

"e70246"

Kód UT WoS článku

001577597000001

EID výsledku v databázi Scopus

2-s2.0-105016997472