A new descriptor of amino acids based on the three dimensional vector of atomic interaction field

• Published in: Chinese science bulletin 2006-03, Vol.51 (5), p.524-529
• Main Authors: Zhou, Peng, Zhou, Yuan, Wu, Shirong, Li, Bo, Tian, Feifei, Li, Zhiliang
• Format: Article
• Language: English
• Subjects: Amino acid sequence; Amino acids; Atomic interactions; Bradykinin; Correlation coefficient; Correlation coefficients; Electrostatic properties; Pentapeptides; Principal components analysis; Structure-activity relationships; 主成分分析; 偏最小二乘回归; 原子间相互作用力场; 多重回归分析; 定量构效关系; 氨基酸; 结构信息; 量子化学
• ISSN: 1001-6538; 2095-9273; 1861-9541; 2095-9281
• DOI: 10.1007/s11434-006-0524-7

A noval molecular structural expression method, three-dimensional vector of atomic interaction field （3D-VAIF）, has been newly developed based on electrostatic and steric interaction between different types of atoms. Feature descriptors of single amino acid, i.e. principal component scores of structural information for amino acids （SSIA）, are obtained through calculation of structural information of 20 coded amino acids using principal component analysis （PCA） method, and the strict tests are performed on the property of SSIA by three quantitative structure-activity relationships （QSARs）/quantitative sequence-activity models （QSAMs） models of 58 ngiotensin-converting enzymes （ACE）, 48 bitter tasting thresholds （BTT） and 31 bradykinin potentiating pentapeptides （BPP）. Cumulative multiple correlation coefficients （E^2cum） are 0.789, 0.856 and 0.838; and corresponding cross-validated correlation coefficients （Q^2Loo） are 0.773, 0.837 and 0.815, respectively. Good results indicate that SSIA are better than traditional descriptors of amino acid in quantitative sequence-activity relationships of peptide analogues.