CYCLOPEp 生成器:通过用户友好型网络平台促进环肽和纳米管研究

IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Alfonso Cabezón , Fabián Suárez-Lestón , Juan R. Granja , Ángel Piñeiro , Rebeca Garcia-Fandino
{"title":"CYCLOPEp 生成器:通过用户友好型网络平台促进环肽和纳米管研究","authors":"Alfonso Cabezón ,&nbsp;Fabián Suárez-Lestón ,&nbsp;Juan R. Granja ,&nbsp;Ángel Piñeiro ,&nbsp;Rebeca Garcia-Fandino","doi":"10.1016/j.csbj.2024.05.044","DOIUrl":null,"url":null,"abstract":"<div><p>The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at <span>http://cyclopep.com/</span><svg><path></path></svg></p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":null,"pages":null},"PeriodicalIF":4.4000,"publicationDate":"2024-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024001892/pdfft?md5=e402d6fd21dd2d604ec1bb1695841fa1&pid=1-s2.0-S2001037024001892-main.pdf","citationCount":"0","resultStr":"{\"title\":\"CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform\",\"authors\":\"Alfonso Cabezón ,&nbsp;Fabián Suárez-Lestón ,&nbsp;Juan R. Granja ,&nbsp;Ángel Piñeiro ,&nbsp;Rebeca Garcia-Fandino\",\"doi\":\"10.1016/j.csbj.2024.05.044\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at <span>http://cyclopep.com/</span><svg><path></path></svg></p></div>\",\"PeriodicalId\":10715,\"journal\":{\"name\":\"Computational and structural biotechnology journal\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":4.4000,\"publicationDate\":\"2024-06-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2001037024001892/pdfft?md5=e402d6fd21dd2d604ec1bb1695841fa1&pid=1-s2.0-S2001037024001892-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational and structural biotechnology journal\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2001037024001892\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational and structural biotechnology journal","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2001037024001892","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

环肽(CPs)和自组装环肽纳米管(SCPNs)的研究对于推动生物医学、纳米电子学和催化等不同领域的应用至关重要。认识到这些分子实验研究的局限性,本文介绍了 CYCLOPEp Builder,这是一种基于网络的综合应用,旨在促进 CPs 和 SCPNs 的设计、模拟和可视化。该工具可生成分子拓扑结构,这对于进行从全原子到粗粒分辨率的分子动力学模拟至关重要。CYCLOPEp Builder 的用户友好界面简化了复杂的分子建模过程,使研究人员能够轻松构建 CP 和 SCPN。该平台功能多样,配备了各种力场,能够生成从单个 CP 到具有不同序列的复杂 SCPN 的结构,并提供平行和反平行取向。CYCLOPEp Builder 增强了分子组装的详细可视化能力,从而提高了对 CP 和 SCPN 分子相互作用的理解。该工具在实现复杂模拟的民主化方面向前迈进了一步,为从事超分子结构探索的科学界提供了宝贵的资源。CYCLOPEp 可通过 http://cyclopep.com/ 访问。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform

The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at http://cyclopep.com/

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Computational and structural biotechnology journal
Computational and structural biotechnology journal Biochemistry, Genetics and Molecular Biology-Biophysics
CiteScore
9.30
自引率
3.30%
发文量
540
审稿时长
6 weeks
期刊介绍: Computational and Structural Biotechnology Journal (CSBJ) is an online gold open access journal publishing research articles and reviews after full peer review. All articles are published, without barriers to access, immediately upon acceptance. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. Specific areas of interest include, but are not limited to: Structure and function of proteins, nucleic acids and other macromolecules Structure and function of multi-component complexes Protein folding, processing and degradation Enzymology Computational and structural studies of plant systems Microbial Informatics Genomics Proteomics Metabolomics Algorithms and Hypothesis in Bioinformatics Mathematical and Theoretical Biology Computational Chemistry and Drug Discovery Microscopy and Molecular Imaging Nanotechnology Systems and Synthetic Biology
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信