title: A large-scale structural classification of antimicrobial peptides.
abstract: Antimicrobial peptides (AMPs) are potent drug candidates against microbial organisms such as bacteria, fungi, parasites, and viruses. AMPs have abundant sequences and structures, two fundamental resources for bioinformatics researches, but analyses on how they associate with each other are either nonexistent or limited to partial classification and data. We thus present A Database of Anti-Microbial peptides (ADAM), which contains 7,007 unique sequences and 759 structures, to systematically establish comprehensive associations between AMP sequences and structures through structural folds and to provide an easy access to view their relationships. 30 distinct AMP structural fold clusters with more than one structure are detected and about a thousand AMPs are associated with at least one structural fold cluster. According to ADAM, AMP structural folds are limited-AMPs only cover about 3% of the overall protein fold space.
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan.
authors.forename: Hao-Ting
authors.identifier: 0000-0001-8284-1572
authors.initials: HT
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan.
authors.forename: Chen-Che
authors.initials: CC
authors.lastname: Lee
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan.
authors.forename: Je-Ruei
authors.initials: JR
authors.lastname: Yang
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan.
authors.forename: Jim Z C
authors.initials: JZ
authors.lastname: Lai
authors.affiliation: Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung 202, Taiwan.
authors.forename: Kuan Y
authors.identifier: 0000-0002-2262-5218
authors.initials: KY
authors.lastname: Chang
mesh_terms: D023181:Antimicrobial Cationic Peptides / Q000737:chemistry*; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid
chemical_list: D023181:Antimicrobial Cationic Peptides