Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi-110020, India.
Comput Biol Med. 2021 Jun;133:104391. doi: 10.1016/j.compbiomed.2021.104391. Epub 2021 Apr 10.
Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of this rapidly expanding field, there is no dedicated resource to study peptide nanostructures. This study endeavours to create a repository of short peptides, which may prove to be the best models to study ordered nanostructures formed by peptide self-assembly. SAPdb has a repertoire of 1049 entries of experimentally validated nanostructures formed by the self-assembly of small peptides. It consists of 328 tripeptides, 701 dipeptides, and 20 single amino acids with some conjugate partners. Each entry encompasses comprehensive information about the peptide, such as chemical modifications, the type of nanostructure formed, experimental conditions like pH, temperature, solvent required for the self-assembly, etc. Our analysis indicates that peptides containing aromatic amino acids favour the formation of self-assembling nanostructures. Additionally, we observed that these peptides form different nanostructures under different experimental conditions. SAPdb provides this comprehensive information in a hassle-free tabulated manner at a glance. User-friendly browsing, searching, and analysis modules have been integrated for easy data retrieval, data comparison, and examination of properties. We anticipate SAPdb to be a valuable repository for researchers engaged in the burgeoning arena of nanobiotechnology. It is freely available at https://webs.iiitd.edu.in/raghava/sapdb.
由肽自组装产生的纳米结构产生了纳米材料，由于其低细胞毒性和对靶向细胞的更高摄取率，因为它们对细胞表面受体具有高亲和力和特异性，因此具有许多治疗应用，包括药物输送和生物医学工程。尽管这个快速发展的领域具有广阔的前景，但目前还没有专门的资源来研究肽纳米结构。本研究旨在创建一个短肽库，这些短肽可能被证明是研究由肽自组装形成的有序纳米结构的最佳模型。SAPdb 拥有由小肽自组装形成的实验验证的纳米结构的 1049 个条目。它包含 328 个三肽、701 个二肽和 20 个单氨基酸，其中一些与共轭物结合。每个条目都包含有关肽的综合信息，例如化学修饰、形成的纳米结构类型、自组装所需的实验条件，如 pH 值、温度、溶剂等。我们的分析表明，含有芳香族氨基酸的肽有利于自组装纳米结构的形成。此外，我们观察到这些肽在不同的实验条件下形成不同的纳米结构。SAPdb 以简洁的表格形式提供了这些全面的信息，一目了然。集成了用户友好的浏览、搜索和分析模块，用于轻松的数据检索、数据比较和特性检查。我们预计 SAPdb 将成为从事蓬勃发展的纳米生物技术领域的研究人员的宝贵资源库。它可以在 https://webs.iiitd.edu.in/raghava/sapdb 免费获取。
