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A novel vector of topological and structural information for amino acids and its QSAR applications for peptides and analogues

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Abstract

A new descriptor, called vector of topological and structural information for coded and noncoded amino acids (VTSA), was derived by principal component analysis (PCA) from a matrix of 66 topological and structural variables of 134 amino acids. The VTSA vector was then applied into two sets of peptide quantitative structure-activity relationships or quantitative sequence-activity modelings (QSARs/QSAMs). Molded by genetic partial least squares (GPLS), support vector machine (SVM), and immune neural network (INN), good results were obtained. For the datasets of 58 angiotensin converting enzyme inhibitors (ACEI) and 89 elastase substrate catalyzed kinetics (ESCK), the R 2, cross-validation R 2, and root mean square error of estimation (RMSEE) were as follows: ACEI, R 2cu ⩾0.82, Q 2cu ⩾0.77, E rmse⩽0.44 (GPLS+SVM); ESCK, R 2cu ⩾0.84, Q 2cu ⩾0.82, E rmse⩽0.20 (GPLS+INN), respectively.

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Authors and Affiliations

  1. College of Chemistry and Chemical Engineering/College of Bioengineering, Chongqing University, Chongqing, 400044, China

    ZhiLiang Li, GenRong Li, Mao Shu, JiaYing Sun, ShanBin Yang, Hu Mei, MengJun Zhang, Ping Zhou, ShiRong Wu, GuoHua Chen, FengLin Lu & TingTing Lu

  2. State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Universiry, Changsha, 410082, China

    ZhiLiang Li, GenRong Li, Mao Shu, JiaYing Sun, MengJun Zhang, Ping Zhou, ShiRong Wu, GuoHua Chen & TingTing Lu

  3. College of Medical Laboratory, Third Military Medical University, Chongqing, 400038, China

    ShanBin Yang, MengJun Zhang, FengLin Lu & TingTing Lu

  4. Life Sciences Technology Centre, Singapore Polytechnic, 500 Dover Road, Singapore, 139651, Singapore

    Hu Mei

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  1. ZhiLiang Li
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  2. GenRong Li
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  3. Mao Shu
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Correspondence to Hu Mei.

Additional information

Supported by the Foundations of National High Technology (863) Programme (Grant No. 2006AA02Z312), State New Drug Project (Grant No. 1996ND1035A01), Fok-Yingtung Educational Foundation (Grant No. 980706), State Key Laboratory of Chemo/Biosensing and Chemometrics Foundation (Grant No. KLCB005-0012), Chongqing University Innovation Fund (Grant No. CUIF030506), Chongqing Municipality Applied Science Fund (Grant No. CASF01-3-6) and Momentous Juche Innovation Fund for Tackle Key Problem Items (Grant No. MJIF 06-9-9)

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Li, Z., Li, G., Shu, M. et al. A novel vector of topological and structural information for amino acids and its QSAR applications for peptides and analogues. Sci. China Ser. B-Chem. 51, 946–957 (2008). https://doi.org/10.1007/s11426-008-0040-5

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  • DOI: https://doi.org/10.1007/s11426-008-0040-5

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