{"title":"Toward a Monte Carlo simulation of protein systems in amino-acid sequence space.","authors":"Yuko Okamoto","doi":"10.1063/5.0240764","DOIUrl":null,"url":null,"abstract":"<p><p>In this article, we present our strategy for studying amino-acid sequence dependences on protein structures. For this purpose, performing Metropolis Monte Carlo simulations in the amino-acid sequence space is necessary. We want to use a coarse-grained protein model with an accurate potential energy function. We introduce a method for optimizing potential-energy parameters based on the native protein structure database, Protein Data Bank.</p>","PeriodicalId":15313,"journal":{"name":"Journal of Chemical Physics","volume":"162 11","pages":""},"PeriodicalIF":3.1000,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Physics","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1063/5.0240764","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 0
Abstract
In this article, we present our strategy for studying amino-acid sequence dependences on protein structures. For this purpose, performing Metropolis Monte Carlo simulations in the amino-acid sequence space is necessary. We want to use a coarse-grained protein model with an accurate potential energy function. We introduce a method for optimizing potential-energy parameters based on the native protein structure database, Protein Data Bank.
期刊介绍：
The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance.
Topical coverage includes:
Theoretical Methods and Algorithms
Advanced Experimental Techniques
Atoms, Molecules, and Clusters
Liquids, Glasses, and Crystals
Surfaces, Interfaces, and Materials
Polymers and Soft Matter
Biological Molecules and Networks.
京公网安备 11010802042870号
京ICP备2023020795号-1
分享
求助内容：
应助结果提醒方式：
扫码关注我们
