Improved methods for classification, prediction, and design of antimicrobial peptides.
Improved methods for classification, prediction, and design of antimicrobial peptides.
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DOI：
10.1007/978-1-4939-2285-7_3
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Wang G
中科院分区：
文献类型：
--
作者：
Wang G
具有不同氨基酸序列、结构和功能的多肽是生物系统中的重要角色。构建标注良好的数据库不仅有助于有效的信息管理、搜索和挖掘，而且还为开发和测试新的多肽算法和机器奠定了基础。抗菌肽数据库在数据库设计和多肽条目方面都是一个原创性的构建。在apd注册的寄主防御抗菌肽(AMPs)涵盖了五个领域(细菌、原生动物、真菌、植物和动物)或三个生命领域(细菌、古菌和真核生物)。这个全面的数据库(http://aps.unmc.edu/AP))提供了关于肽发现时间表、命名、分类、词汇表、计算工具和统计数据的有用信息。Apd可以有效地搜索、预测和设计具有抗菌、抗病毒、抗真菌、抗寄生虫、杀虫、杀精、抗癌、趋化、免疫调节或抗氧化特性的多肽。本文提出了一种通用的分类方案，以统一来自各种生物来源的天然免疫肽。作为一项改进，升级的apd基于数据库定义的参数空间进行预测，并提供与自然AMP最相似的序列列表。此外，数据库搜索引擎强大的流水线设计为设计新型抗菌剂以对抗具有耐药性的超级细菌、病毒、真菌或寄生虫奠定了坚实的基础。这个全面的AMP数据库对于研究和教育都是一个有用的工具。
Peptides with diverse amino acid sequences, structures and functions are essential players in biological systems. The construction of well-annotated databases not only facilitates effective information management, search and mining, but also lays the foundation for developing and testing new peptide algorithms and machines. The antimicrobial peptide database (APD) is an original construction in terms of both database design and peptide entries. The host defense antimicrobial peptides (AMPs) registered in the APD cover the five kingdoms (bacteria, protists, fungi, plants, and animals) or three domains of life (bacteria, archaea, and eukaryota). This comprehensive database (http://aps.unmc.edu/AP) provides useful information on peptide discovery timeline, nomenclature, classification, glossary, calculation tools, and statistics. The APD enables effective search, prediction, and design of peptides with antibacterial, antiviral, antifungal, antiparasitic, insecticidal, spermicidal, anticancer activities, chemotactic, immune modulation, or anti-oxidative properties. A universal classification scheme is proposed herein to unify innate immunity peptides from a variety of biological sources. As an improvement, the upgraded APD makes predictions based on the database-defined parameter space and provides a list of the sequences most similar to natural AMPs. In addition, the powerful pipeline design of the database search engine laid a solid basis for designing novel antimicrobials to combat resistant superbugs, viruses, fungi or parasites. This comprehensive AMP database is a useful tool for both research and education.