程孟辉



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近期发表文章
  • Using auto covariance method for functional discrimination of membrane proteins based on evolution information

  • Amino Acids,(2010) 38:1497–1503

    Li Yang  , Yizhou Li  , Rongquan Xiao  , Yuhong Zeng  , JiaMin Xiao  , Fuyuan Tan  , Menghui Chen

    Abstract:  

    Membrane transporters are critical in living cells. Therefore, the discrimination of the types of membrane proteins based on their functions is of great importance both for helping genome annotation and providing a supplementary role to experimental researchers to gain insight into membrane proteins’ function. There are a lot of computational methods to facilitate the identification of the functional types of membrane proteins. However, in these methods, the local sequence environment was not integrated into the constructed model. In this study, we described a new strategy to predict the functional types of membrane proteins using a model based on auto covariance and position-specific scoring matrix. The novelty of the presented approach is considering the distribution of different positions of functional conservation sites in protein sequences. Thereby, this model adequately takes into account the long-range correlation between such sites during sequential evolution. Fivefold cross-validation test shows that this method greatly improves the prediction
    accuracy and achieves an acceptable prediction accuracy of 87.51%. The result indicates that the current approach might be an effective tool for predicting the functional
    types of membrane proteins only using the primary sequences. The code and dataset used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/
    predict_membrane.zip.



  • Substituent Effects on the Hydrogen-bonded Complex of Aniline-H2O: A Computational Study

  • New J. Chem,32, 1060-1070

    Menghui Chen  , Xuemei Pu*  , Ning-Bew Wong  , Menglong Li  , Anmin Tian 

    Abstract:  

    Substituent effects (X = -CH3, -NH2, -OH, -F, -SiH3, -PH2, -H, -Cl, -CN, -NO2, -CHO) on the hydrogen-bonded complex of para-substituted aniline with one water molecule are studied at the B3LYP/6-311 + + G(d,p) level of theory. The nature of H-bond interactions and the origin of substituent effects are explored by means of natural bond orbital (NBO) and atoms in molecules (AIM) analysis as well as a series of good correlation equations obtained. The result suggests that the substitution induces changes in the electron density transfer from the water molecule to the aniline derivative by means of influencing the interaction of no → σ*N-H while the change in the electron density transfer would give rise to the variation on the electron densities in the proton donating N-H bond and the N-H···O hydrogen bond, and ultimately, influence the length and the frequency of the N-H bond, the H··· O distance, the binding energies of complexes, the pKa of the substituted aniline and the 1H chemical shift. In addition, the correlations obtained reveals that the H-bond parameters calculated (such as ∇2ρH...O, ρH...O, RH...O), reflecting both the intramolecular (substituent effects) and intermolecular (water effects) interactions, are found to perform better than substituent constants in rationalizing the substitution induced variations on the structure, the binding energy, 1H chemical shift and experimental pKa.