Kuo Chen Chou

Summary

Publications

  1. ncbi request reprint Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, Torrey Del Mar Drive, San Diego, California 92130, USA
    J Cell Biochem 91:1197-203. 2004
  2. doi request reprint Prediction and analysis of protein palmitoylation sites
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Biochimie 93:489-96. 2011
  3. doi request reprint Three new powerful oseltamivir derivatives for inhibiting the neuraminidase of influenza virus
    Shu Qing Wang
    School of Pharmaceutical Sciences, Tianjin Medical University, Tianjin, China
    Biochem Biophys Res Commun 401:188-91. 2010
  4. ncbi request reprint Molecular modeling of cytochrome P450 and drug metabolism
    Jing Fang Wang
    Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai 200240, China
    Curr Drug Metab 11:342-6. 2010
  5. ncbi request reprint Recent progress in protein subcellular location prediction
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Anal Biochem 370:1-16. 2007
  6. doi request reprint Some remarks on predicting multi-label attributes in molecular biosystems
    Kuo Chen Chou
    Gordon Life Science Institute, 53 South Cottage Road, Belmont, Massachusetts 02478, USA
    Mol Biosyst 9:1092-100. 2013
  7. pmc Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, PR China
    BMC Bioinformatics 11:293. 2010
  8. pmc A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, USA
    PLoS ONE 5:e9931. 2010
  9. pmc iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, United States of America
    PLoS ONE 6:e18258. 2011
  10. pmc Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization
    Kuo Chen Chou
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
    PLoS ONE 5:e11335. 2010

Collaborators

Detail Information

Publications129 found, 100 shown here

  1. ncbi request reprint Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, Torrey Del Mar Drive, San Diego, California 92130, USA
    J Cell Biochem 91:1197-203. 2004
    ....
  2. doi request reprint Prediction and analysis of protein palmitoylation sites
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Biochimie 93:489-96. 2011
    ..Meanwhile, the protein disorder region might also play an import role in the post-translational modification. These findings may provide useful insights for revealing the mechanisms of palmitoylation...
  3. doi request reprint Three new powerful oseltamivir derivatives for inhibiting the neuraminidase of influenza virus
    Shu Qing Wang
    School of Pharmaceutical Sciences, Tianjin Medical University, Tianjin, China
    Biochem Biophys Res Commun 401:188-91. 2010
    ..Or at the very least, the findings may stimulate new strategy or provide useful insights for working on the target vitally important to the health of human beings...
  4. ncbi request reprint Molecular modeling of cytochrome P450 and drug metabolism
    Jing Fang Wang
    Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai 200240, China
    Curr Drug Metab 11:342-6. 2010
    ..It is important to further understand why a certain genotype influences enzyme activity and how to predict more structure-activity relationships...
  5. ncbi request reprint Recent progress in protein subcellular location prediction
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Anal Biochem 370:1-16. 2007
  6. doi request reprint Some remarks on predicting multi-label attributes in molecular biosystems
    Kuo Chen Chou
    Gordon Life Science Institute, 53 South Cottage Road, Belmont, Massachusetts 02478, USA
    Mol Biosyst 9:1092-100. 2013
    ..The current mini review focuses on the recent progresses in this area from both conceptual aspects and detailed mathematical formulations...
  7. pmc Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, PR China
    BMC Bioinformatics 11:293. 2010
    ....
  8. pmc A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, USA
    PLoS ONE 5:e9931. 2010
    ..It is anticipated that the novel approach and the powerful predictor as presented in this paper will have a significant impact to Molecular Cell Biology, System Biology, Proteomics, Bioinformatics, and Drug Development...
  9. pmc iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, United States of America
    PLoS ONE 6:e18258. 2011
    ....
  10. pmc Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization
    Kuo Chen Chou
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China
    PLoS ONE 5:e11335. 2010
    ..It is anticipated that the Plant-mPLoc predictor as presented in this paper will become a very useful tool in plant science as well as all the relevant areas...
  11. doi request reprint iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California 92130, USA
    Mol Biosyst 8:629-41. 2012
    ....
  12. ncbi request reprint Graphic rule for drug metabolism systems
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    Curr Drug Metab 11:369-78. 2010
    ..g., according to their directed graphs, the metabolism of seliciclib and the metabolism of vildagliptin can be categorized as 0-->5 mechanism while that of AG-024322 as 0-->4-->3 mechanism...
  13. ncbi request reprint MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 360:339-45. 2007
    ..As a Web server, MemType-2L is freely accessible to the public at http://chou.med.harvard.edu/bioinf/MemType...
  14. doi request reprint Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA
    Nat Protoc 3:153-62. 2008
    ..The computational time for each prediction is less than 5 s in most cases. The Cell-PLoc package is freely accessible at http://chou.med.harvard.edu/bioinf/Cell-PLoc...
  15. doi request reprint ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information
    Kuo Chen Chou
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
    Biochem Biophys Res Commun 376:321-5. 2008
    ..The overall success rates in both cases by rigorous cross-validation tests were higher than 92%. ProtIdent is freely accessible to the public as a web server at http://www.csbio.sjtu.edu.cn/bioinf/Protease...
  16. doi request reprint Some remarks on protein attribute prediction and pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    J Theor Biol 273:236-47. 2011
    ....
  17. ncbi request reprint Using supervised fuzzy clustering to predict protein structural classes
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Biochem Biophys Res Commun 334:577-81. 2005
    ....
  18. ncbi request reprint Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 347:150-7. 2006
    ..And the current predictor is one of these kinds, and has proved to be a very powerful one. The Hum-PLoc classifier is available as a web-server at http://202.120.37.186/bioinf/hum...
  19. ncbi request reprint Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Bioinformatics 21:10-9. 2005
    ..Although the results were quite encouraging, the entire prediction process was based on the amino acid composition alone without including any sequence-order information. Therefore, it is worthy of further investigation...
  20. ncbi request reprint Prediction of protein signal sequences and their cleavage sites by statistical rulers
    Hui Liu
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 200030, China
    Biochem Biophys Res Commun 338:1005-11. 2005
    ..It is anticipated that the mutual information approach introduced here may be very useful for studying many other sequence-coupling problems in molecular biology as well...
  21. ncbi request reprint Molecular insights of SAH enzyme catalysis and implication for inhibitor design
    Huachun Wei
    College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
    J Theor Biol 244:692-702. 2007
    ..0.1 software. Then we discussed about the mechanism of the inhibition reaction, followed by proposing the potential inhibitors by comparing best docked solutions and possible modification for the best inhibitors...
  22. ncbi request reprint Ensemble classifier for protein fold pattern recognition
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Bioinformatics 22:1717-22. 2006
    ..Their outcomes were combined through a weighted voting to give a final determination for classifying a query protein. The recognition was to find the true fold among the 27 possible patterns...
  23. ncbi request reprint Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands
    Dong Qing Wei
    College of Life Science and Technology, Shanghai Jiaotong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
    Biochem Biophys Res Commun 344:1048-55. 2006
    ..Such a finding might provide insights into the secret why some of H5N1 strains bear high resistance for existing NA inhibitors, and stimulate new strategies for designing new drugs against these viruses...
  24. ncbi request reprint Prediction of protein subcellular locations by GO-FunD-PseAA predictor
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 320:1236-9. 2004
    ..The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure...
  25. ncbi request reprint A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 311:743-7. 2003
    ..the biological objective to which the gene or gene product contributes, (2). the biochemical activity of a gene product, and (3). the place in the cell where a gene product is active...
  26. doi request reprint iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins
    Wei Zhong Lin
    Information Science and Technology School, Donghua University, Shanghai, 200261, China
    Mol Biosyst 9:634-44. 2013
    ..As a user-friendly web-server, iLoc-Animal is freely accessible to the public at the web-site ...
  27. ncbi request reprint Using protein-protein interaction network information to predict the subcellular locations of proteins in budding yeast
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Protein Pept Lett 19:644-51. 2012
    ..As a user-friendly web-server, Yeast-PLoc is freely accessible at http://yeastloc.biosino.org/...
  28. ncbi request reprint Agaritine and its derivatives are potential inhibitors against HIV proteases
    Wei Na Gao
    College of Life Science and Technology, Shanghai Jiaotong University, 800 Donglin Road, Minhang District, Shanghai, China
    Med Chem 3:221-6. 2007
    ....
  29. ncbi request reprint Predicting 22 protein localizations in budding yeast
    Yu Dong Cai
    Biomolecular Sciences Department, UMIST, P O Box 88, Manchester M60 1QD, UK Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 323:425-8. 2004
    ..It is anticipated that the augmented GO-FunD-PseAA predictor will become a very useful tool in predicting protein subcellular localization for both basic research and practical application...
  30. ncbi request reprint Insights from modeling the tertiary structure of human BACE2
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California 92130, USA
    J Proteome Res 3:1069-72. 2004
    ....
  31. ncbi request reprint Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS
    Kuo Chen Chou
    Gordon Life Science Institute, 7088 Arbor Valley, Kalamazoo, MI 49009, USA
    Biochem Biophys Res Commun 308:148-51. 2003
    ..Meanwhile, the idea of how to develop inhibitors of the SARS enzyme based on the knowledge of its own peptide substrates (the so-called "distorted key" approach) was also briefly elucidated...
  32. ncbi request reprint Using GO-PseAA predictor to identify membrane proteins and their types
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 327:845-7. 2005
    ..84%. The high success rates suggest that the GO-PseAA predictor can catch the core feature of the statistical samples concerned and may become an automated high throughput toll in molecular and cell biology...
  33. ncbi request reprint Computational studies of the binding mechanism of calmodulin with chrysin
    Lin Li
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
    Biochem Biophys Res Commun 358:1102-7. 2007
    ..These findings may shed light upon the binding interactions of CaM with chrysin, providing a solid molecular basis for subset analysis of its pharmacological benefits...
  34. ncbi request reprint Predicting membrane protein types by the LLDA algorithm
    Tong Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, 200030, China
    Protein Pept Lett 15:915-21. 2008
    ..Our jackknife and independent dataset test results indicate that it is very promising to use the LLDA approach to cope with complicated problems in biological systems, such as predicting the membrane protein type...
  35. doi request reprint Improving the accuracy of predicting disulfide connectivity by feature selection
    Lin Zhu
    Department of Bioinformatics, Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
    J Comput Chem 31:1478-85. 2010
    ..All these findings provide important insights for structural studies of disulfide-rich proteins...
  36. ncbi request reprint iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints
    Xuan Xiao
    Computer Department, Jing De Zhen Ceramic Institute, Jing De Zhen 333403, China Information School, Zhe Jiang Textile and Fashion College, Ning bo 315211, China Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA 02478, United States Electronic address
    J Theor Biol 337:71-9. 2013
    ..It has not escaped our notice that the current approach can also be used to study other drug-target interaction networks. ..
  37. ncbi request reprint Support vector machine for predicting alpha-turn types
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, China
    Peptides 24:629-30. 2003
    ....
  38. ncbi request reprint Weighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition
    Meng Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Protein Eng Des Sel 17:509-16. 2004
    ....
  39. ncbi request reprint Predicting protein subcellular location by fusing multiple classifiers
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, California 92130, USA
    J Cell Biochem 99:517-27. 2006
    ..The fusion ensemble classifier will be available at www.pami.sjtu.edu.cn/people/hbshen...
  40. ncbi request reprint Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types
    Hongbin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Biochem Biophys Res Commun 334:288-92. 2005
    ..The OET-KNN classifier will be available as a web-server at http://www.pami.sjtu.edu.cn/kcchou...
  41. ncbi request reprint Predicting protein localization in budding yeast
    Kuo Chen Chou
    Gordon Life Science Institute San Diego, CA 92130, USA
    Bioinformatics 21:944-50. 2005
    ..The present study was initiated in an attempt to address (1) how to efficiently identify the localization of a query protein among many possible subcellular locations, and (2) how to deal with the case of multiplex locations...
  42. ncbi request reprint A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis
    Meng Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Med Chem 1:39-47. 2005
    ..Such a discovery can be used to rapidly and reliably diagnose SARS coronavirus for both basic research in laboratories and practical application in clinics...
  43. ncbi request reprint SLLE for predicting membrane protein types
    Meng Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 200030, China
    J Theor Biol 232:7-15. 2005
    ..The current approach represents a new strategy to deal with the problems of protein attribute prediction, and hence may become a useful vehicle in the area of bioinformatics and proteomics...
  44. ncbi request reprint Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 200030 Shanghai, China
    J Theor Biol 240:9-13. 2006
    ..The novel approach may also have notable impact on prediction of the other attributes, such as protein structural class, protein subcellular localization, and enzyme family class, among many others...
  45. ncbi request reprint Prediction and classification of protein subcellular location-sequence-order effect and pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    J Cell Biochem 90:1250-60. 2003
    ..It is anticipated that the current automated method can be developed to a high throughput tool for practical usage in both basic research and pharmaceutical industry...
  46. ncbi request reprint A novel approach to predict active sites of enzyme molecules
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California, USA
    Proteins 55:77-82. 2004
    ..It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics...
  47. ncbi request reprint Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP
    Jing Fang Wang
    Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
    Biochem Biophys Res Commun 359:323-9. 2007
    ....
  48. ncbi request reprint Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, 200233, China
    J Cell Biochem 84:343-8. 2002
    ..Furthermore, tests for correct prediction rates were undertaken with three independent testing datasets containing 2,148 proteins, 2,417 proteins, and 2,494 proteins producing values of 84, 77, and 74%, respectively...
  49. doi request reprint A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
    Anal Biochem 394:269-74. 2009
    ..As a consequence, the prediction power has been significantly enhanced. The web server of Hum-mPLoc2.0 is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/hum-multi-2/...
  50. ncbi request reprint 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design
    Jing Fang Wang
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
    Biochem Biophys Res Commun 355:513-9. 2007
    ....
  51. ncbi request reprint PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition
    Hong Bin Shen
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Anal Biochem 373:386-8. 2008
    ..Here, we present a web-server called PseAAC at http://chou.med.harvard.edu/bioinf/PseAA/, by which users can generate various kinds of PseAA composition to best fit their need...
  52. doi request reprint Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
    J Theor Biol 264:326-33. 2010
    ..5%, which was more than 14% higher than the corresponding rate by the Gneg-PLoc. As a user friendly web-server, Gneg-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/...
  53. pmc iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking
    Xuan Xiao
    Computer Department, Jing De Zhen Ceramic Institute, Jing De Zhen, China Information School, ZheJiang Textile and Fashion College, Ningbo, China Gordon Life Science Institute, Belmont, Massachusetts, United States of America
    PLoS ONE 8:e72234. 2013
    ..It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug - target interaction networks. ..
  54. ncbi request reprint Computational methods for protein-protein interaction and their application
    Tie Liu Shi
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Curr Protein Pept Sci 6:443-9. 2005
    ..This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed...
  55. ncbi request reprint Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 1954 Hua Shan Road, Shanghai 200030, China
    Protein Eng Des Sel 20:561-7. 2007
    ..As a user-friendly web-server, Nuc-PLoc is freely accessible to the public at http://chou.med.harvard.edu/bioinf/Nuc-PLoc...
  56. ncbi request reprint Large-scale predictions of gram-negative bacterial protein subcellular locations
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA
    J Proteome Res 5:3420-8. 2006
    ..The large-scale results will be updated twice a year to cover the new entries of Gram-negative bacterial proteins and reflect the new development of Gneg-PLoc...
  57. ncbi request reprint Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 357:633-40. 2007
    ..Signal-CF is freely available as a web-server at http://chou.med.harvard.edu/bioinf/Signal-CF/ or http://202.120.37.186/bioinf/Signal-CF/...
  58. ncbi request reprint Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA
    J Proteome Res 5:1888-97. 2006
    ..A web server, called "Euk-OET-PLoc", has been designed at http://202.120.37.186/bioinf/euk-oet for public to predict subcellular locations of eukaryotic proteins by the fusion OET-KNN classifier...
  59. ncbi request reprint Signal-3L: A 3-layer approach for predicting signal peptides
    Hong Bin Shen
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 363:297-303. 2007
    ..The large-scale file is prepared with Microsoft Excel and named "Tab-Signal-3L.xls", and will be updated once a year to include new protein entries and reflect the continuous development of Signal-3L...
  60. ncbi request reprint Using a new alignment kernel function to identify secretory proteins
    Hui Liu
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 200030, China
    Protein Pept Lett 14:203-8. 2007
    ..The novel approach can be effectively used to extract the statistical properties of protein sequences for machine learning, leading to a higher prediction success rate...
  61. ncbi request reprint Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, CA 92130, USA
    J Proteome Res 4:1681-6. 2005
    ..The findings may also provide useful insights for stimulating new therapeutic approaches by manipulating the interaction of the receptor with the relevant G proteins...
  62. ncbi request reprint Prediction of protease types in a hybridization space
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 339:1015-20. 2006
    ..36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics...
  63. ncbi request reprint Molecular therapeutic target for type-2 diabetes
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    J Proteome Res 3:1284-8. 2004
    ..On the basis of the docking results, a binding pocket of human GFAT1 dimer for UDP-GlcNAc is defined. All of these findings can serve as a reference or footing in developing new therapeutic strategy for the treatment of type-2 diabetes...
  64. ncbi request reprint Methodology development for predicting subcellular localization and other attributes of proteins
    Hong Bin Shen
    Shanghai Jiaotong University, Institute of Image Processing and Pattern Recognition, Shanghai, China
    Expert Rev Proteomics 4:453-63. 2007
    ..Meanwhile, an outline of the use of different descriptors for protein samples is given. In addition, a series of web servers established recently based on various ensemble classifiers are also briefly introduced...
  65. ncbi request reprint Progress in protein structural class prediction and its impact to bioinformatics and proteomics
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California 92130, USA
    Curr Protein Pept Sci 6:423-36. 2005
    ..Also, some promising approaches for the further development of protein structural class prediction are also addressed...
  66. doi request reprint QuatIdent: a web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
    J Proteome Res 8:1577-84. 2009
    ..csbio.sjtu.edu.cn/bioinf/Quaternary/ , by which one can get the desired 2-level results for a query protein sequence in around 25 seconds. The longer the sequence is, the more time that is needed...
  67. ncbi request reprint Predicting protein quaternary structure by pseudo amino acid composition
    Kuo Chen Chou
    Gordon Life Science Institute, Kalamazoo, Michigan 49009, USA
    Proteins 53:282-9. 2003
    ..Results obtained by resubstitution, jack-knife, and independent data set tests, have indicated that the current approach might be quite promising in dealing with such an extremely complicated and difficult problem...
  68. ncbi request reprint Prediction of protein secondary structure content by artificial neural network
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, 200233, China
    J Comput Chem 24:727-31. 2003
    ..C. Chou [J Protein Chem 1999, 18, 473] was adopted as the input. Self-consistency and independent-dataset tests were used to appraise the performance of the neural network. Results of both tests indicated high performance of the method...
  69. ncbi request reprint Gpos-mPLoc: a top-down approach to improve the quality of predicting subcellular localization of Gram-positive bacterial proteins
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
    Protein Pept Lett 16:1478-84. 2009
    ..2%, which was about 10% higher than the corresponding rate by the Gpos-PLoc. As a user friendly web-server, Gpos-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gpos-multi/...
  70. ncbi request reprint EzyPred: a top-down approach for predicting enzyme functional classes and subclasses
    Hong Bin Shen
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 364:53-9. 2007
    ..EzyPred is freely accessible at http://chou.med.harvard.edu/bioinf/EzyPred/, by which one can get the desired 3-level results for a query protein sequence within less than 90 s...
  71. pmc Predicting drug-target interaction networks based on functional groups and biological features
    Zhisong He
    CAS MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 5:e9603. 2010
    ..As a complement, the in silico prediction methods can provide us with very useful information in a timely manner...
  72. ncbi request reprint Structural bioinformatics and its impact to biomedical science
    Kuo Chen Chou
    Shanghai Jiaotong University, Life Science Research Center, Shanghai 200030, China
    Curr Med Chem 11:2105-34. 2004
    ..Also, the limitation of these approaches and the future challenges of structural bioinformatics are briefly addressed...
  73. ncbi request reprint Structure of cytochrome p450s and personalized drug
    Jing Fang Wang
    College of Life and Biotechnology, Shanghai Tong University, Shanghai, China
    Curr Med Chem 16:232-44. 2009
    ..With the help of computational methods, the structural information will provide insights into personalization of drug treatments in both proper drug therapy and appropriate dosage of a certain drug...
  74. ncbi request reprint Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 1954 Hua Shan Road, Shanghai 200030, China
    Biopolymers 85:233-40. 2007
    ..xls." This file is available at the same website and will be updated twice a year to include the new entries of viral proteins and reflect the continuous development of Virus-PLoc...
  75. doi request reprint HIVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins
    Hong Bin Shen
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Anal Biochem 375:388-90. 2008
    ..med.harvard.edu/bioinf/HIV/. In this note we provide a step-to-step guide for how to use HIVcleave to identify the cleavage sites of a query protein sequence by HIV-1 and HIV-2 proteases, respectively...
  76. ncbi request reprint Predicting protein structural class by functional domain composition
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 321:1007-9. 2004
    ..This indicates that using the functional domain composition to represent the sample of a protein for statistical prediction is very promising, and that the functional type of a domain is closely correlated with its structural class...
  77. doi request reprint Predicting protein fold pattern with functional domain and sequential evolution information
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
    J Theor Biol 256:441-6. 2009
    ..The PFP-FunDSeqE predictor is freely available to the public as a web server at http://www.csbio.sjtu.edu.cn/bioinf/PFP-FunDSeqE/...
  78. ncbi request reprint Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism
    Jing Fang Wang
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China
    Med Chem 5:263-70. 2009
    ....
  79. ncbi request reprint Prediction of membrane protein types by incorporating amphipathic effects
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, California 92130, USA
    J Chem Inf Model 45:407-13. 2005
    ..The success rates thus obtained have been remarkably enhanced in identifying the types of membrane proteins, as demonstrated by the jackknife test and independent data set test, respectively...
  80. ncbi request reprint Predicting protein-protein interactions from sequences in a hybridization space
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, California 92130, USA
    J Proteome Res 5:316-22. 2006
    ..6%, indicating the GO-PseAA predictor is very promising for predicting protein-protein interactions from protein sequences, and might become a useful vehicle for studying the network biology in the postgenomic era...
  81. pmc Prediction of protein domain with mRMR feature selection and analysis
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 7:e39308. 2012
    ..Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine...
  82. ncbi request reprint A pharmacophore model specific to active site of CYP1A2 with a novel molecular modeling explorer and CoMFA
    Tao Zhang
    State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P R 200240, China
    Med Chem 8:198-207. 2012
    ..It is anticipated that our approach can be extended to investigate the protein-ligand interactions for many other enzyme-catalyzed systems as well...
  83. ncbi request reprint A novel sequence-based method for phosphorylation site prediction with feature selection and analysis
    Zhi Song He
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences SIBS, Chinese Academy of Sciences CAS, Shanghai, China
    Protein Pept Lett 19:70-8. 2012
    ..64%, 66.11%% and 66.69%, respectively. These rates were obtained by rigorous jackknife cross-validation tests...
  84. ncbi request reprint Insights from modeling the 3D structure of DNA-CBF3b complex
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, CA 92130, USA
    J Proteome Res 4:1657-60. 2005
    ..The model also provides a footing for further considering the possible binding arrangements of the other three subunits, namely CBF3a, CBF3c, and CBF3d...
  85. pmc Predicting enzyme family class in a hybridization space
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Protein Sci 13:2857-63. 2004
    ..The corresponding rates by the independent data set test were 98% and 97%, respectively...
  86. doi request reprint Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations
    Jing Fang Wang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Biochem Biophys Res Commun 390:608-12. 2009
    ..These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association...
  87. doi request reprint iLoc-Virus: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites
    Xuan Xiao
    Computer Department, Jing De Zhen Ceramic Institute, Jing De Zhen, China
    J Theor Biol 284:42-51. 2011
    ..It is anticipated that iLoc-Virus may become a useful high throughput tool for both basic research and drug development...
  88. ncbi request reprint Identification of proteins interacting with human SP110 during the process of viral infections
    Lei Cai
    Key Laboratory of Systems Biomedicine Ministry of Education, Shanghai Centre for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
    Med Chem 7:121-6. 2011
    ..These findings may provide useful insights into the development of new drugs for treating and preventing intracellular pathogen diseases...
  89. ncbi request reprint Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR)
    Qing hua Liao
    Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, PR China
    Med Chem 7:24-31. 2011
    ..It is anticipated that the findings reported here may provide very useful information or clue for designing effective drugs for the therapeutic treatment of EGFR-related cancer...
  90. doi request reprint GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions
    Xuan Xiao
    Computer Department, Jing De Zhen Ceramic Institute, Jing De Zhen 333403, China
    Mol Biosyst 7:911-9. 2011
    ..It is anticipated that GPCR-2L may become a useful tool for both basic research and drug development in the areas related to GPCRs...
  91. doi request reprint Identification of proteases and their types
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200240, China
    Anal Biochem 385:153-60. 2009
    ..Finally, the essence of why ProtIdent can yield a high success rate in identifying proteases and their types is elucidated...
  92. ncbi request reprint Using maximum entropy model to predict protein secondary structure with single sequence
    Yong Sheng Ding
    College of Information Sciences and Technology, Donghua University, Shanghai, China
    Protein Pept Lett 16:552-60. 2009
    ....
  93. ncbi request reprint Virus-mPLoc: a fusion classifier for viral protein subcellular location prediction by incorporating multiple sites
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
    J Biomol Struct Dyn 28:175-86. 2010
    ..For reader's convenience, a user-friendly web-server for Virus-mPLoc was designed that is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/virus-multi/...
  94. ncbi request reprint Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition
    Shuang Quan Wang
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200240, China
    J Theor Biol 242:941-6. 2006
    ..The stacked generalization classifier is available as a web-server named "SG-MPt_Pred" at: http://202.120.37.186/bioinf/wangsq/service.htm...
  95. doi request reprint Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus
    Jing Fang Wang
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
    Biochem Biophys Res Commun 388:413-7. 2009
    ..The findings and the relevant analysis reported here might provide useful structural insights for developing effective drugs against the new swine flu virus...
  96. ncbi request reprint Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition
    Hong Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
    Biochem Biophys Res Commun 337:752-6. 2005
    ..The OET-KNN classifier will be available at www.pami.sjtu.edu.cn/people/hbshen...
  97. ncbi request reprint Low-frequency Fourier spectrum for predicting membrane protein types
    Hui Liu
    Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai 200030, China
    Biochem Biophys Res Commun 336:737-9. 2005
    ..The novel approach also holds a high potential for predicting many other attributes of proteins...
  98. ncbi request reprint Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar Drive, San Diego, California 92130, USA kchou san rr com
    J Proteome Res 6:1728-34. 2007
    ....
  99. ncbi request reprint Using GO-PseAA predictor to predict enzyme sub-class
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 325:506-9. 2004
    ....
  100. ncbi request reprint Large-scale plant protein subcellular location prediction
    Kuo Chen Chou
    Gordon Life Science Institute, San Diego, CA 92130, USA
    J Cell Biochem 100:665-78. 2007
    ..The large-scale results will be updated twice a year to include new entries of plant proteins and reflect the continuous development of Plant-PLoc...
  101. ncbi request reprint Modeling the tertiary structure of human cathepsin-E
    Kuo Chen Chou
    Gordon Life Science Institute, 13784 Torrey Del Mar, San Diego, CA 92130, USA
    Biochem Biophys Res Commun 331:56-60. 2005
    ..The computed three-dimensional structure of cathepsin-E and the relevant findings might provide useful insights for designing inhibitors with the desired selectivity...