ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues.
In this study, structural topology scale (ST-scale) was recruited as a novel structural topological descriptor derived from principal component analysis on 827 structural variables of 167 amino acids. By using partial least squares (PLS), we applied ST-scale for the study of quantitative sequence-activity models (QSAMs) on three peptide datasets (58 angiotensin-converting enzyme (ACE) inhibitors, 34 antimicrobial peptides (AMPs) and 89 elastase substrates (ES)). The results of QSAMs were superior to that of the earlier studies, with determination coefficient (r(2)) and cross-validated (q(2)) equal to 0.855, 0.774; 0.79, 0.371 (OSC-PLS: 0.995, 0.848) and 0.846, 0.747, respectively. Therefore, ST-scale descriptors were considered to be competent to extract information from 827 structural variables and relate with their bioactivities.
Yang
Li
L
Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, 400030 Chongqing, People's Republic of China.
Shu
Mao
M
Ma
Kaiwang
K
Mei
Hu
H
Jiang
Yongjun
Y
Li
Zhiliang
Z
D000596:Amino Acids / Q000737:chemistry*; D000806:Angiotensin-Converting Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D000890:Anti-Infective Agents / Q000737:chemistry / Q000494:pharmacology; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry / Q000494:pharmacology; D001185:Artificial Intelligence; D030562:Databases, Protein; D004151:Dipeptides / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008956:Models, Chemical; D010196:Pancreatic Elastase / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D012984:Software; D013211:Staphylococcus aureus / Q000187:drug effects; D013223:Statistics as Topic; D013552:Swine
D000596:Amino Acids; D000806:Angiotensin-Converting Enzyme Inhibitors; D000890:Anti-Infective Agents; D023181:Antimicrobial Cationic Peptides; D004151:Dipeptides; D010455:Peptides; D010196:Pancreatic Elastase