CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform

被引:0
|
作者
Cabezon, Alfonso [1 ]
Suarez-Leston, Fabian [1 ,2 ,3 ]
Granja, Juan R. [1 ]
Pineiro, Angel [2 ]
Garcia-Fandino, Rebeca [1 ]
机构
[1] Univ Santiago De Compostela, Ctr Res Biol Chem & Mol Mat, Dept Organ Chem, CIQUS, Santiago De Compostela, Spain
[2] Univ Santiago De Compostela, Fac Phys, Dept Appl Phys, Soft Matter & Mol Biophys Grp, Santiago De Compostela, Spain
[3] MD USE Innovat SL, Edificio Emprendia, Santiago De Compostela 15782, Spain
来源
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL | 2024年 / 25卷
关键词
Cyclic peptides; Self-assembling cyclic peptide nanotubes; (SCPNs); Molecular; Builder; Supramolecular structures; Molecular dynamics simulations; FORCE-FIELD; SIMULATIONS; PROTEINS;
D O I
10.1016/j.csbj.2024.05.044
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 webbased 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/
引用
收藏
页码:91 / 94
页数:4
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