HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome

Abstract

\n\n Antimicrobial peptides (AMPs) can defend the hosts against various\npathogens and are found in almost every life form from microorganisms to humans. As the rapid\nincrease of drug-resistant strains in recent years is presenting a serious challenge to healthcare,\nantimicrobial peptides (AMPs) can revolutionize the antimicrobial development against the drugresistant\nmicrobes.\n\n\n\nThe objective was to encourage the study on the human microbiome towards the\ninhibition of drug-resistant bacteria by the development of a database containing antimicrobial\npeptides from the human microbiome.\n\n\n\n This database is an outcome of an extended analysis of human metagenome, involving\nthe prediction of coding regions, extraction of peptides, prediction of antimicrobial peptides, and\nmodeling their structure utilizing different in silico tools. Furthermore, an intelligent hash\nfunction-based query engine was designed to validate the novelty of specific candidate peptide\nover the reported Knowledge-base.\n\n\n\n This Knowledge-base currently focuses on antimicrobial peptide\nsequences (AMPs) predicted from the human microbiome along with their 3D structures modeled\nusing various modeling and molecular dynamics approaches. It includes a total of 1087 unique\nAMPs from various body sites, with 454 AMPs from the oral cavity, 180 AMPs from the\ngastrointestinal tract, 42 AMPs from the skin, 12 AMPs from the airway, 6 AMPs from the\nurogenital tract and 393 AMPs from undefined body locations. A scoring matrix has been\ngenerated based on the similarity scores of the sequences that have been incorporated into the\nKnowledge-base. Furthermore, a Jmol applet is included in the website to help users visualize the\n3D structures.\n\n\n\nThe information and functions of the Knowledge-base can offer great help in finding\nnovel antimicrobial drugs, especially towards finding inhibitors for drug-resistant bacteria. The\nHAMP is freely available at https://bioserver.iiita.ac.in/amp/index.html.\n