The Antimicrobial Peptide Database (APD3) is a comprehensive resource for research and education on natural antimicrobial peptides (AMPs). Initially launched in 2003, APD3 has been regularly updated and expanded since 2009. It contains 2619 AMPs, including 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic, and 185 anticancer peptides. The database includes annotations for various functions such as antibiofilm, antimalarial, antiprotist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant, and protease inhibiting properties. It also provides searchable annotations for target pathogens, molecule-binding partners, post-translational modifications, and animal models. The APD3 features a user-friendly interface with advanced search capabilities, including peptide sequence search, chemical modifications, peptide parameters, structure classifications, and additional tools for peptide prediction and design. The database includes information on the source organism, peptide activity, and structure, as well as statistical data on AMPs. The APD3 also provides educational resources, including web pages for teaching, a glossary, FAQs, and a timeline of AMP discoveries. The database is used for various applications in research and education, including peptide property calculations, classification methods, identification of similar sequences, AMP statistics, cleavage sequence selection, structure-activity relationship studies, and peptide design. The APD3 is a valuable resource for researchers and educators in the field of antimicrobial peptides, offering a comprehensive database for peptide discovery, nomenclature, classification, information search, calculations, prediction, and design. The database is continuously updated and expanded, and it is accessible online at http://aps.unmc.edu/AP.The Antimicrobial Peptide Database (APD3) is a comprehensive resource for research and education on natural antimicrobial peptides (AMPs). Initially launched in 2003, APD3 has been regularly updated and expanded since 2009. It contains 2619 AMPs, including 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic, and 185 anticancer peptides. The database includes annotations for various functions such as antibiofilm, antimalarial, antiprotist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant, and protease inhibiting properties. It also provides searchable annotations for target pathogens, molecule-binding partners, post-translational modifications, and animal models. The APD3 features a user-friendly interface with advanced search capabilities, including peptide sequence search, chemical modifications, peptide parameters, structure classifications, and additional tools for peptide prediction and design. The database includes information on the source organism, peptide activity, and structure, as well as statistical data on AMPs. The APD3 also provides educational resources, including web pages for teaching, a glossary, FAQs, and a timeline of AMP discoveries. The database is used for various applications in research and education, including peptide property calculations, classification methods, identification of similar sequences, AMP statistics, cleavage sequence selection, structure-activity relationship studies, and peptide design. The APD3 is a valuable resource for researchers and educators in the field of antimicrobial peptides, offering a comprehensive database for peptide discovery, nomenclature, classification, information search, calculations, prediction, and design. The database is continuously updated and expanded, and it is accessible online at http://aps.unmc.edu/AP.