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Scores of amino acid 0D-3D information as applied in cleavage site prediction and better specificity elucidation for human immunodeficiency virus type 1 protease

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Science China Chemistry 2008年第8期51卷 794-800页

作者： KANG liFang liANG GuiZhao SHU Mao YANG ShanBin li zhiliang College of Bioengineering Chongqing UniversityChongqing 400030China College of Chemistry and Chemical Engineering Chongqing UniversityChongqing 400030China

A new set of descriptors,namely score vectors of the zero dimension,one dimension,two dimensions and three dimensions(SZOTT),was derived from principle component analysis of a matrix of 1369 structural variables including 0D,1D,2D and 3D information for the 20 coded amino acids. SZOTT scales were then used in cleavage site prediction of human immunodeficiency virus type 1 protease. linear discriminant analysis(LDA) and support vector machines(SVM) were applied to developing models to predict the cleavage sites. The results obtained by linear discriminant analysis(LDA) and support vector machines(SVM) are as follows. The Matthews correlation coefficients(MCC) by the resubstitution test,leave-one-out cross validation(LOOCV) and external validation are 0.879 and 0.911,0.849 and 0.901,0.822 and 0.846,respectively. The receiver operating characteristic(ROC) analysis showed that the SVM model possesses better simulative and predictive ability in comparison with the LDA model. Satisfactory results show that SZOTT descriptors can be further used to predict cleavage sites of human immunodeficiency virus type 1 protease.

关键词： score vector of zero dimension one dimension two dimensions and three dimensions(SZOTT) human immunodeficiency virus type 1 protease(HIV PR) linear discriminant analysis(LDA) support vector machine(SVM)

Support vector machine applied in QSAR modelling

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Chinese Science Bulletin 2005年第20期50卷 2291-2296页

作者： MEI Hu ZHOU Yuan liANG Guizhao li zhiliang College of Chemistry and Chemical Engineering Chongqing University Chongqing 400044 China Key Laboratory of Biomedical Engineering of Ministry of Education and Chongqing City Chongqing 400044 China College of Bioengineering. Chongqing University Chongqing 400044 China

Support vector machine (SVM), partial least squares (PLS), and Back-Propagation artificial neural net- work (ANN) were employed to establish QSAR models of 2 dipeptide datasets. In order to validate predictive capabilities on external dataset of the resulting models, both internal and external validations were performed. The division of dataset into both training and test sets was carried out by D-optimal design. The results showed that support vector machine (SVM) behaved well in both calibration and prediction. For the dataset of 48 bitter tasting dipeptides (BTD), the results obtained by support vector regression (SVR) were superior to that by PLS in both calibration and prediction. When compared with BP artificial neural network, SVR showed less calibration power but more predictive capability. For the dataset of angiotensin-converting enzyme (ACE) inhibitors, the results obtained by support vector machine (SVM) re- gression were equivalent to those by PLS and BP artificial neural network. In both datasets, SVR using linear kernel function behaved well as that using radial basis kernel func- tion. The results showed that there is wide prospect for the application of support vector machine (SVM) into QSAR modeling.

关键词：支撑向量装置 SVM 最小二乘法 QSAR模型人工神经网络

A novel comparative molecule/pseudo receptor interaction analysis

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Chinese Science Bulletin 2006年第15期51卷 1824-1829页

作者： ZHOU Peng TONG Jianbo TIAN Feifei li zhiliang College of Chemistry and Chemical Engineering Chongqing University Chongqing 400044 China Key Laboratory of Biomedical Engineering of Ministry of Education Chongqing 400044 China College of Chemistry and Chemical Engineering Shanxi University Taiyuan 030006 China

Comparative molecule/pseudo receptor interaction analysis (CoMPIA) is developed as a novel 3D-QSAR method by adding postulated pseudo receptor and GA-optimized probe into com- parative molecular field analysis (CoMFA). CoMPIA is used to find the pseudo receptor mode by opti- mizing probe distributions and to establish the opti- mal model of high qualities and good interpretations. Correlative coefficient R2, cross-validated correlative coefficient Q2 and root mean square error RMSEP of the resulting model are 0.940, 0.868 and 0.502, re- spectively by applying CoMPIA to quantitative struc- ture-activity relationship (QSAR) of 31 classical ster- oids.

关键词： CoMPIA 3D-QSAR CoMFA 分析化学

Mapping and validation of the epistatic D and P genes controlling anthocyanin biosynthesis in the peel of eggplant (Solanum melongena L.) fruit

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Horticulture Research 2023年第2期10卷 181-193页

作者： Qian You Huimin li Jun Wu Tao li Yikui Wang Guangwen Sun zhiliang li Baojuan Sun Guangdong Key Laboratory for New Technology Research of Vegetables Vegetable Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong 510640China College of Horticulture South China Agricultural UniversityGuangzhouGuangdong 510642China Institute of Vegetable Guangxi Academy of Agricultural SciencesNanningGuangxi 530007China Ganzhou Research Institute of Vegetables and Flowers Gannan Academy of SciencesGanzhouJiangxi 341400China

Fruit color is an important trait inf luencing the commercial value of eggplant *** dominant genes(D,P and Y)cooperatively control the anthocyanin coloration in eggplant fruits,but none has been *** this study,two white-fruit accessions(19141 and 19147)and their F2 progeny,with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits,were used for mapping the D and P genes.A high-density genetic map was constructed with 5270 SNPs spanning 1997.98 *** QTLs were identified,including two genes on chromosome 8 and one on chromosome *** expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D,*** further identified(1)a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19141,(2)a G base InDel in the promoter region leading to an additional cis-regulatory element and(3)a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1,in ***,these three variations were validated by PARMS technology as related to phenotypes in the F2 ***,silencing of SmANS or SmMYB1 in the purple red fruits of F1(E3316)led to inhibition of anthocyanin biosynthesis in the ***,overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19141 and 19147 *** findings demonstrated the epistatic interactions underlying the white color of eggplant fruits,which can be potentially applied to breeding of eggplant fruit peel color.

关键词： breeding plant white

Applying generalized hydrophobicity scale of amino acids to quantitative prediction of human leukocyte antigen-A~*0201-restricted cytotoxic T lymphocyte epitope

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Chinese Science Bulletin 2006年第12期51卷 1439-1443页

作者： ZHOU Peng TIAN Feifei ZHANG Mengjun li zhiliang College of Chemistry and Chemical Engineering Chongqing University Chongqing 400044 China State Key Laboratory of Chemo/Biosensing and Chemometdcs Changsha 410082 China Department of Medical Analysis Third Surgeon University Chongqing 400044 China

Derived from 149 hydrophobic factors of 20 natural amino acids, a novel amino acid descriptor termed as generalized hydrophobicity scale (GH-scale) was proposed by principal component analysis (PCA). Via genetic algorithm-partial least square (GPLS) method, quantitative structure-activity relationship (QSAR) model was constructed by GH-scale for 152 human leukocyte antigen (HLA)-A*0201-restricted cytotoxic T lymphocyte (CTL) epitopes with the model estimated and cross-validated correlative coefficients of R2 = 0.813 and Q2 = 0.725, respectively. It was in- dicated that hydrophobic interaction played an im- portant role in HLA-A*0201-CTL interaction, promi- nently at anchor residues.

关键词：疏水性氨基酸 CTL抗原决定基遗传算法白细胞抗原 T淋巴细胞

A NEW APPROACH OF SIMULTANEOUS FAULTS DIAGNOSIS BASED ON RANDOM SETS AND DSMT

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Journal of Electronics(China) 2009年第1期26卷 24-30页

作者： li zhiliang Xu Xiaobin Wen Chenglin Institute of Information and Control Hangzhou Dianzi University Hangzhou 310018 China

Simultaneous faults often occur in running equipments, in order to solve the problems of the simultaneous faults, a new approach based on random sets and Dezert-Smarandache Theory (DSmT) is proposed in this paper. Firstly, the simultaneous faults' model is built based on the generalized frame of discernment in DSmT. Secondly, according to the unified description of combination rules in evidence reasoning based on random sets, a new combination rule for simultaneous faults diagnosis is proposed. Thirdly, according to the working characteristics and environment of the sensors used to acquire fault characteristic information, a new method to construct basic probability assignment function is pro- posed based on membership. Finally, diagnosis result is obtained by use of the new combination rule combined with decision rules. A case pertaining to the fault diagnosis for a multi-function rotor test-bed is given, and the result shows that the proposed diagnosis approach is feasible and efficient.

关键词： Random sets Dezert-Smarandache Theory (DSmT) Basic probability assignment Simultaneous fault Diagnosis

Using scores of amino acid topological descriptors for quantitative sequence-mobility modeling of peptides based on support vector machine

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Chinese Science Bulletin 2006年第22期51卷 2700-2705页

作者： liANG Guizhao YANG Shanbin ZHOU Yuan ZHOU Peng li zhiliang Key Laboratory for Biomechanics and Tissue Engineering of Ministry of Education Chongqing 400030 China College of Chemistry and Chemical Engineering Chongqing University Chongqing 400030 China State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan University Changsha 410082 China

拓扑的描述符(SATD ) 从与 23 氨基酸有关的 1262 个结构的变量的一个矩阵的原则部件分析导出的氨基酸的分数被采用在不同长度表示 125 肽的结构。量的 sequence-mobilitymodelings (QSMM ) 用部分最少的平方被构造(请) 并且支持向量机... 详细信息

拓扑的描述符(SATD ) 从与 23 氨基酸有关的 1262 个结构的变量的一个矩阵的原则部件分析导出的氨基酸的分数被采用在不同长度表示 125 肽的结构。量的 sequence-mobilitymodelings (QSMM ) 用部分最少的平方被构造(请) 并且支持向量机器(SVM ) 分别地。作为新氨基酸规模，包括与生物活性有关的丰富的信息的 SATD 容易被操作。更好的结果与获得与的那些相比被获得请，它显示 SVM 介绍了柔韧的稳定性和优秀预兆的能力 forelectrophoretic 活动性。这些结果证明在 QSMM 为应用 ofSATD 和 SVM 回归有宽前景。

关键词：氨基酸 SATD 电泳迁移率 QSMM SVM

A novel molecular distance edge vector as applied to chemical modeling of quantitative structure-retention relationships:Various gas chromatographic retention behaviors of polychlorinated dibenzofurans on different polarity-varying stationary phases

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Chinese Science Bulletin 2005年第16期50卷 1683-1687页

作者： DENG Hong HUANG Ping HU Yinyu YE Nancy li zhiliang College of Chemistry and Chemical Engineering Key Laboratory of Biomedical Engineering of Chongqing Municipality and Center for Molecular Modeling and Drug Designing Chongqing University Chongqing 400044 China Key Laboratory of Biomechanical Engineering of Education Ministry Department of Chemical Biology and Molecular Toxicology Institute of Biomedical Engineering Chongqing University Chongqing 400044 China

Based on the identical group as a pseudo atom instead of a typical atom, a novel modified molecular dis-tance-edge (MDE) vector μ was developed in our laboratory to characterize chemical structure of polychlorinated diben-zofurans (PCDFs) congeners and/or isomers. Quantitative structure-retention relationships (QSRRs) between the new VMDE parameters and gas chromatographic (GC) retention behavior of PCDFs were then generated by multiple linear regression (MLR) method for non-polar, moderately polar, and polar stationary phases. Four excellent models with high correlation coefficients, R=0.984-0.995, were proposed for non-polar columns (DB-5, SE-54, OV-101). For the moder-ately polar columns (OV-1701), the correlation coefficient of the developed good model is only 0.958. For the polar col-umns (SP-2300), the QSRR model is poor with R=0.884. Then cross validation with leave-one out of procedure (CV) is performed in high correlation with the non-polar (Rcv=992-0.974) and weakly polar (Rcv=921) columns and in little cor-relation (Rcv=0.834) with the polar columns. These results show that the new μ vector is suitable for describing the re-tention behaviors of PCDFs on non-polar and moderately polar stationary phases and not for the various gas chroma-tographic retention behaviors of PCDFs on the different po-larity-varying stationary phases.

关键词：分子距离向量 MDE 氧芴分子模型化学结构异构体

Improving electrical and thermal properties synchronously via introducing CsPbBr_(3)QDs into higher manganese silicides

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Journal of Materials Science & Technology 2022年第16期111卷 279-286页

作者： Qing Wang zhiliang li Xiaofeng Yang Xin Qian linjuan Guo Jianglong Wang Dan Zhang Shu-Fang Wang Key Laboratory of High-precision Computation and Application of Quantum Field Theory of Hebei Province College of Physics Science and TechnologyHebei UniversityBaoding 071002China Hebei Key Lab of Optic-Electronic Information and Materials College of Physics Science and TechnologyHebei UniversityBaoding 071002China

Higher manganese silicide(HMS)is a P-type medium temperature thermoelectric(TE)material,which has attracted widespread attention over the past few decades due to its remarkable mechanical properties,excellent chemical and thermal stability,as well as the non-toxicity,abundance and competitive *** peak power factor(PF)of HMS is as high as~1.50×10^(-3)W m^(-1)K^(-2)because of its intrinsic high electrical conductivity and Seebeck ***,the thermal conductivity of HMS is also high,resulting in relatively low z T *** nano-dispersion in the matrix is one of the most effective methods to enhance the TE properties via reducing the lattice thermal conductivity significantly without drastic changes on the other *** this study,Cs Pb BrQDs with uniform size were synthesized and introduced into HMS *** PF(at 823 K)was enhanced to 1.71×10^(-3)W m^(-1)K^(-2),which is improved 14.0%approximately compared with that of pure HMS owing to the combined effect of element doping and energy *** lattice thermal conductivity(at 823 K)decreased from 2.56W mKto 1.99 W mKsynchronously(~22.0%)due to the intensive phonon scattering caused by Cs doping,and the embedding of Pb riched CsPbBr_(3)QDs and Pb QDs.A maximum z T value of 0.57(823 K)is achieved in Cs Pb BrQDs/HMS composites,which is 36.0%higher than that of pure ***,for other TE materials,it is also feasible to improve the TE properties via introducing metastable quantum dots.

关键词： Thermoelectric material Higher manganese silicide Quantum dot Figure of merit Inclusion