TY - JOUR
T1 - dbAMP 3.0
T2 - updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
AU - Yao, Lantian
AU - Guan, Jiahui
AU - Xie, Peilin
AU - Chung, Chia Ru
AU - Zhao, Zhihao
AU - Dong, Danhong
AU - Guo, Yilin
AU - Zhang, Wenyang
AU - Deng, Junyang
AU - Pang, Yuxuan
AU - Liu, Yulan
AU - Peng, Yunlu
AU - Horng, Jorng Tzong
AU - Chiang, Ying Chih
AU - Lee, Tzong Yi
N1 - Publisher Copyright:
© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2025/1/6
Y1 - 2025/1/6
N2 - Antimicrobial resistance is one of the most urgent global health threats, especially in the post-pandemic era. Antimicrobial peptides (AMPs) offer a promising alternative to traditional antibiotics, driving growing interest in recent years. dbAMP is a comprehensive database offering extensive annotations on AMPs, including sequence information, functional activity data, physicochemical properties and structural annotations. In this update, dbAMP has curated data from over 5200 publications, encompassing 33,065 AMPs and 2453 antimicrobial proteins from 3534 organisms. Additionally, dbAMP utilizes ESMFold to determine the three-dimensional structures of AMPs, providing over 30,000 structural annotations that facilitate structure-based functional insights for clinical drug development. Furthermore, dbAMP employs molecular docking techniques, providing over 100 docked complexes that contribute useful insights into the potential mechanisms of AMPs. The toxicity and stability of AMPs are critical factors in assessing their potential as clinical drugs. The updated dbAMP introduced an efficient tool for evaluating the hemolytic toxicity and half-life of AMPs, alongside an AMP optimization platform for designing AMPs with high antimicrobial activity, reduced toxicity and increased stability. The updated dbAMP is freely accessible at https://awi.cuhk.edu.cn/dbAMP/. Overall, dbAMP represents a comprehensive and essential resource for AMP analysis and design, poised to advance antimicrobial strategies in the post-pandemic era.
AB - Antimicrobial resistance is one of the most urgent global health threats, especially in the post-pandemic era. Antimicrobial peptides (AMPs) offer a promising alternative to traditional antibiotics, driving growing interest in recent years. dbAMP is a comprehensive database offering extensive annotations on AMPs, including sequence information, functional activity data, physicochemical properties and structural annotations. In this update, dbAMP has curated data from over 5200 publications, encompassing 33,065 AMPs and 2453 antimicrobial proteins from 3534 organisms. Additionally, dbAMP utilizes ESMFold to determine the three-dimensional structures of AMPs, providing over 30,000 structural annotations that facilitate structure-based functional insights for clinical drug development. Furthermore, dbAMP employs molecular docking techniques, providing over 100 docked complexes that contribute useful insights into the potential mechanisms of AMPs. The toxicity and stability of AMPs are critical factors in assessing their potential as clinical drugs. The updated dbAMP introduced an efficient tool for evaluating the hemolytic toxicity and half-life of AMPs, alongside an AMP optimization platform for designing AMPs with high antimicrobial activity, reduced toxicity and increased stability. The updated dbAMP is freely accessible at https://awi.cuhk.edu.cn/dbAMP/. Overall, dbAMP represents a comprehensive and essential resource for AMP analysis and design, poised to advance antimicrobial strategies in the post-pandemic era.
UR - https://www.scopus.com/pages/publications/85214378703
U2 - 10.1093/nar/gkae1019
DO - 10.1093/nar/gkae1019
M3 - Article
C2 - 39540425
AN - SCOPUS:85214378703
SN - 0305-1048
VL - 53
SP - D364-D376
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -