Design of proteins by parallel tempering in the sequence space
The result's identifiers
Result code in 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>
Result on the web
<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>
Alternative languages
Result language
angličtina
Original language name
Design of proteins by parallel tempering in the sequence space
Original language description
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.
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10608 - Biochemistry and molecular biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
PROTEIN SCIENCE
ISSN
0961-8368
e-ISSN
1469-896X
Volume of the periodical
34
Issue of the periodical within the volume
10
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
"e70246"
UT code for WoS article
001577597000001
EID of the result in the Scopus database
2-s2.0-105016997472