title: Comprehensive comparison of twenty structural characterization scales applied as QSAM of antimicrobial dodecapeptides derived from Bac2A against P. aeruginosa.
abstract: Informative numerical characterizations of amino acid residues are essential for quantitative sequence-activity modeling (QSAM). To date, a variety of structural characterization methods based on local amino acids have been proposed. However, limited detailed reports are available using same datasets and modeling methods to compare the ability to characterize structures of amino acids. Here, we evaluate the characterization capability of 20 descriptor sets on a set of antimicrobial peptides (AMPs) derived from Bac2A against P. aeruginosa. Results display the models by FASGAI, z-scales, VHSE, DPPS, HESH and ProtFP descriptors present qualified predictive capability. Moreover, the structural characterization of the studied AMPs should involve the hydrophobic, bulky and electronic properties of amino acids; besides, the secondary structural information should not be ignored. In parallel, the FASGAI-based model exhibits a more robust prediction than other models, and reasonably describe the structure-activity relationship of the studied dodecapeptides, which is in line with the reported experimental observations. This work provides references for methods of structural characterization as applied in QSAM of AMPs against P. aeruginosa.
authors.affiliation: Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Qian
authors.affiliation: Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China.
authors.forename: Ya'nan
authors.initials: Y
authors.lastname: Liang
authors.affiliation: Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China.
authors.forename: Wanqian
authors.initials: W
authors.lastname: Liu
authors.affiliation: Key Laboratory of Biorheological Science and Technology, Ministry of Education, School of Bioengineering, Chongqing University, Chongqing 400044, PR China. Electronic address: gzliang@cqu.edu.cn.
authors.forename: Guizhao
authors.initials: G
authors.lastname: Liang
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000890:Anti-Infective Agents / Q000737:chemistry*; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions / Q000187:drug effects; D008958:Models, Molecular; D011552:Pseudomonas Infections / Q000188:drug therapy / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000737:chemistry / Q000187:drug effects* / Q000472:pathogenicity; D021281:Quantitative Structure-Activity Relationship
chemical_list: D000890:Anti-Infective Agents; D023181:Antimicrobial Cationic Peptides
keywords: Antimicrobial peptides (AMPs); Factor analysis scale of generalized amino acid information (FASGAI); Quantitative sequence-activity modeling (QSAM); Structural characterization