Amino Acids



【Amino Acids】介绍
英文名称:Amino Acids
中文名称:氨基酸,
期刊主页:
出版地:

  Amino Acids publishes contributions from all fields of amino acid research: analysis, separation, synthesis, biosynthesis, cross linking amino acids, racemization/enantiomers, modification of amino acids as phosphorylation, methylation, acetylation, glycosylation and nonenzymatic glycosylation, new roles for amino acids in physiology and pathophysiology, biology, amino acid analogues and derivatives, polyamines, radiated amino acids, peptides, stable isotopes and isotopes of amino acids. Applications in medicine, food chemistry, nutrition, gastroenterology, nephrology, neurochemistry, pharmacology, excitatory amino acids are just some topics to be listed.

Fields of interest:
Biochemistry, food chemistry, nutrition, neurology, psychiatry, pharmacology, nephrology, gastroenterology, microbiology
 


实验室在此刊物上发表的文章
  1. Prediction of mitochondrial proteins based on genetic algorithm – partial least squares and support vector machine

  2. Amino Acids,Volume 33, Number 4, 669-675,

    Fuyuan Tan  , XiaoYu Feng  , Fang Zheng  , Menglong Li*  , Yanzhi Guo  , Lin JIANG 

    Abstract:  

    Mitochondria are essential cell organelles of eukaryotes. Hence, it is vitally important to develop an automated and reliable method for timely identification of novel mitochondrial proteins. In this study, mitochondrial proteins were encoded by dipeptide composition technology; then, the genetic algorithm-partial least square (GA-PLS) method was used to evaluate the dipeptide composition elements which are more important in recognizing mitochondrial proteins; further, these selected dipeptide composition elements were applied to support vector machine (SVM)-based classifiers to predict the mitochondrial proteins. All the models were trained and validated by the jackknife cross-validation test. The prediction accuracy is 85%, suggesting that it performs reasonably well in predicting the mitochondrial proteins. Our results strongly imply that not all the dipeptide compositions are informative and indispensable for predicting proteins. The source code of MATLAB and the dataset are available on request under liml@scu.edu.cn.



  3. Identification of RNA-binding sites in proteins by integrating various sequence information

  4. Amino Acids,s00726-010-0639-7

    CuiCui Wang  , Yaping Fang  , JiaMin Xiao  , Menglong Li

    Abstract:  

    RNA–protein interactions play a pivotal role in various biological processes, such as mRNA processing, protein synthesis, assembly, and function of ribosome. In this work, we have introduced a computational method for predicting RNA-binding sites in proteins based on support vector machines by using a variety of features from amino acid sequence information including position-specific scoring matrix (PSSM) profiles, physicochemical properties and predicted solvent accessibility. Considering the influence of the surrounding residues of an amino acid and the dependency effect from the neighboring amino acids, a sliding window and a smoothing window are used to encode the PSSM profiles. The outer fivefold cross-validation method is evaluated on the data set of 77 RNA-binding proteins (RBP77). It achieves an overall accuracy of 88.66% with the Matthew’s correlation coefficient (MCC) of 0.69. Furthermore, an independent data set of 39 RNA-binding proteins (RBP39) is employed to further evaluate the performance and achieves an overall accuracy of 82.36% with the MCC of 0.44. The result shows that our method has good generalization abilities in predicting RNA-binding sites for novel proteins. Compared with other previous methods, our method performs well on the same data set. The prediction results suggest that the used features are effective in predicting RNA-binding sites in proteins. The code and all data sets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/Predict_RBP.rar.



  5. Using auto covariance method for functional discrimination of membrane proteins based on evolution information

  6. 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.



  7. Predicting DNA-binding proteins: approached from Chou’s pseudo amino acid composition and other specific sequence features

  8. Amino Acids,(2008) 34: 103–109

    Yaping Fang  , Yanzhi Guo  , Yi Feng  , Menglong Li

    Abstract:  

        DNA-binding proteins play a pivotal role in gene regulation.It is vitally important to develop an automated and efficient method for timely identification of novel DNA-binding proteins. In this study, we proposed a method based on alone the primary sequences of proteins to predict the DNA-binding proteins. DNA-binding proteins were encoded by autocross-covariance transform, pseudo-amino acid composition, dipeptide composition, respectively and also the different combinations of the three encoded methods; further, these feature matrices were applied to support vector machine classifiers to predict the DNA-binding proteins. All modules were trained and validated by the jackknife cross-validation test. Through comparing the performance of these substituted modules, the best result was obtained from pseudo-amino acid composition with the overall accuracy of 96.6% and the sensitivity of 90.7%. The results suggest that it can efficiently predict the novel DNA-binding proteins only using the primary sequences.



  9. Delaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition

  10. Amino Acids,

    Zhining Wen  , Lin JIANG  , Yanzhi Guo  , Ke Long Wang 

    Abstract:  

    As an important transmembrane protein family in eukaryon,G-protein coupled receptors (GPCRs) play a significant role in cellular
    signal transduction and are important targets for drug design. However, it is very difficult to resolve their tertiary structure by X-ray crystallography. In this study, we have developed a Delaunay model, which constructs a series of simplexes with latent variables to classify the families of GPCRs and projects unknown sequences to principle component space (PC-space) to predict their topology. Computational results show that, for the classification of GPCRs, the method achieves the accuracy of 91.0 and 87.6% for Class A, more than 80% for the other three classes in differentiating GPCRs from non-GPCRs and 70% for discriminating between four major
    classes of GPCR, respectively. When recognizing the structure of GPCRs, all the N-terminals of sequences can be determined correctly. The maximum accuracy of predicting transmembrane segments is achieved in the 7th transmembrane segment of Rhodopsin, which is 99.4%, and the average error is 2.1 amino acids, which is the lowest in all of the segments prediction. This method could provide structural information of a novel GPCR as a tool for experiments and other algorithms of structure prediction
    of GPCRs. Academic users should send their request for the MATLAB program for classifying GPCRs and predicting the topology
    of them at liml@scu.edu.cn.



  11. Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform

  12. Amino Acids,2006, 30, 397-402

    Yanzhi Guo  , Menglong Li*  , Zhining Wen  , Ke Long Wang 

    Abstract:  

    As the potential drug targets, G-protein coupled receptors (GPCRs) and nuclear receptors (NRs) are the focuses in pharmaceutical
    research. It is of great practical significance to develop an automated and reliable method to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine was proposed to classify GPCRs and NRs from the hydrophobicity of proteins. The models for all the GPCR families and NR subfamilies were trained and validated using jackknife test and the results thus obtained are quite promising.Meanwhile, the performance of the method was evaluated
    on GPCR and NR independent datasets with good performance. The good results indicate the applicability of the method. Two web servers implementing the prediction are available at http:==chem.scu.edu.cn=blast= Pred-GPCR and http:==chem.scu.edu.cn=blast=Pred-NR.