APD3: the antimicrobial peptide database as a tool for research and education
Guangshun Wang,Xia Li,Zhe Wang +2 more
Reads0
Chats0
TLDR
Newly annotated are AMPs with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties and various database applications in research and education are summarized.Abstract:
The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/) is an original database initially online in 2003. The APD2 (2009 version) has been regularly updated and further expanded into the APD3. This database currently focuses on natural antimicrobial peptides (AMPs) with defined sequence and activity. It includes a total of 2619 AMPs with 261 bacteriocins from bacteria, 4 AMPs from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. The APD3 contains 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. Newly annotated are AMPs with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. We also describe other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. Amino acid profiles or signatures of natural AMPs are important for peptide classification, prediction and design. Finally, we summarize various database applications in research and education.read more
Citations
More filters
Journal ArticleDOI
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Baofeng Jia,Amogelang R. Raphenya,Brian Alcock,Nicholas Waglechner,Peiyao Guo,Kara K. Tsang,Briony A. Lago,Biren M. Dave,Sheldon K. Pereira,Arjun N. Sharma,Sachin Doshi,Mélanie Courtot,Raymond Lo,Laura E. Williams,Jonathan G. Frye,Tariq Elsayegh,Daim Sardar,Erin L. Westman,Andrew C. Pawlowski,Timothy A. Johnson,Fiona S. L. Brinkman,Gerard D. Wright,Andrew G. McArthur +22 more
TL;DR: The Comprehensive Antibiotic Resistance Database (CARD) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR.
Journal ArticleDOI
The immunology of host defence peptides: beyond antimicrobial activity
TL;DR: This Review focuses on human HDPs and explores the diverse immunomodulatory effects of HDPs from a systems biology perspective, which highlights the interconnected nature of the effect (or effects) ofHDPs on the host.
Journal ArticleDOI
Antimicrobial host defence peptides: functions and clinical potential
TL;DR: The emerging potential to therapeutically harness cationic host defence peptides to treat infectious diseases, chronic inflammatory disorders and wound healing is assessed, highlighting current preclinical studies and clinical trials.
Journal ArticleDOI
Mechanisms and consequences of bacterial resistance to antimicrobial peptides
TL;DR: Routine clinical administration of AMPs to treat bacterial infections may select for resistant bacterial pathogens capable of better evading the innate immune system, as well as the ramifications of therapeutic levels of exposure on the development of AMP resistance and bacterial pathogenesis.
Journal ArticleDOI
Antimicrobial Peptides: Mechanisms of Action and Resistance:
TL;DR: Recent advances in understanding of the diverse mechanisms of action of cationic AMPs are described and the bacterial resistance against these peptides and the recently developed peptide GL13K is used as an example.
References
More filters
Journal ArticleDOI
A simple method for displaying the hydropathic character of a protein
Jack Kyte,Russell F. Doolittle +1 more
TL;DR: A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised and its simplicity and its graphic nature make it a very useful tool for the evaluation of protein structures.
Journal ArticleDOI
Antimicrobial peptides of multicellular organisms
TL;DR: As the need for new antibiotics becomes more pressing, could the design of anti-infective drugs based on the design principles these molecules teach us?
Journal ArticleDOI
Antimicrobial and host-defense peptides as new anti-infective therapeutic strategies.
TL;DR: The role of cationic host-defense peptides in modulating the innate immune response and boosting infection-resolving immunity while dampening potentially harmful pro-inflammatory (septic) responses gives these peptides the potential to become an entirely new therapeutic approach against bacterial infections.
Journal ArticleDOI
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
Carl R. Woese,George E. Fox +1 more
TL;DR: A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: the eubacteria, comprising all typical bacteria, the archaebacteria, and the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
Journal ArticleDOI
Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor
TL;DR: A family of peptides with broad-spectrum antimicrobial activity has been isolated from the skin of the African clawed frog Xenopus laevis and appears to represent a previously unrecognized class of vertebrate antimicrobial activities.