Protein sequence analysis using relational soft clustering algorithms

References

• Qian , N. and Sejnowski , T. J. 1988 . Predicting the secondary structure of globular proteins using neural network models . Journal of Molecular Biology , 202 : 865 – 884 .
   PubMed Web of Science ®Google Scholar
• Dayhoff , M. O. , Schwartz , R. M. and Orcutt , B. C. 1978 . A model of evolutionary change in proteins. Matrices for detecting distant relationships . Atlas of Protein Sequence and Structure , 5 : 345 – 358 .
   Google Scholar
• Henikoff , S. and Henikoff , J. G. 1992 . Amino acid substitution matrices from protein blocks . PNSA , 89 : 10915 – 10919 .
   PubMed Web of Science ®Google Scholar
• Johnson , M. S. and Overington , J. P. 1993 . A structural basis for sequence comparisons: an evaluation of scoring methodologies . Journal of Molecular Biology , 233 : 716 – 738 .
   PubMed Web of Science ®Google Scholar
• Thomson , R. , Hodgman , C. , Yang , Z. R. and Doyle , A. K. 2003 . Characterising proteolytic cleavage site activity using bio-basis function neural network . Bioinformatics , 19 : 1741 – 1747 .
   PubMed Web of Science ®Google Scholar
• Berry , E. A. , Dalby , A. R. and Yang , Z. R. 2004 . Reduced bio-basis function neural network for identification of protein phosphorylation sites: Comparison with pattern recognition algorithms . Computational Biology and Chemistry , 28 : 75 – 85 .
   PubMedGoogle Scholar
• Yang , Z. R. and Thomson , R. 2005 . Bio-basis function neural network for prediction of protease cleavage sites in proteins . IEEE Transactions on Neural Networks , 16 : 263 – 274 .
   PubMedGoogle Scholar
• Yang , Z. R. 2005 . Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks . Bioinformatics , 21 : 1831 – 1837 .
   PubMedGoogle Scholar
• Yang , Z. R. , Thomson , R. , McNeil , P. and Esnouf , R. 2005 . RONN: Use of the bio-basis function neural network technique for the detection of natively disordered regions in proteins . Bioinformatics , 21 : 3369 – 3376 .
   PubMed Web of Science ®Google Scholar
• Yang , Z. R. and Chou , K. C. 2004 . Predicting the O-linkage sites in glycoproteins using bio-basis function neural networks . Bioinformatics , 20 : 903 – 908 .
   PubMedGoogle Scholar
• Kaufman , L. and Rousseeuw , P. J. 1987 . “ Clustering by means of medoids ” . In Statistical Data Analysis Based on the L₁ Norm , Edited by: Dodge , Y. 405 – 416 . Amsterdam : North Holland/Elsevier .
   Google Scholar
• Kaufman , L. and Rousseeuw , P. J. 1990 . Finding Groups in Data, An Itroduction to Cluster Analysis , Brussels : John Wiley .
   Google Scholar
• Zadeh , L. A. 1965 . Fuzzy sets . Information and Control , 8 : 338 – 353 .
   Web of Science ®Google Scholar
• Pawlak , Z. 1991 . Rough Sets, Theoretical Aspects of Resoning About Data , Dordrecht : Kluwer .
   Google Scholar
• Dubois , D. and Prade , H. 1990 . Rough fuzzy sets and fuzzy rough sets . International Journal of General Systems , 17 : 191 – 209 .
   Web of Science ®Google Scholar
• Saad , P. , Shamsuddin , S. M. , Deris , S. and Mohamad , D. 2002 . Rough set on trademark images for neural network classifier . International Journal of Computer Mathematics , 79 : 789 – 796 .
   Web of Science ®Google Scholar
• Lee , H.-S. and Chou , M.-T. 2004 . Fuzzy forecasting based on fuzzy time series . International Journal of Computer Mathematics , 81 : 781 – 789 .
   Web of Science ®Google Scholar
• Skowron , A. , Swiniarski , R. W. and Synak , P. 2005 . Approximation spaces and information granulation . Transactions on Rough Sets , 3 : 175 – 189 .
   Google Scholar
• Ruspini , E. H. 1970 . Numerical methods for fuzzy clustering . Information Science , 2 : 319 – 350 .
   Web of Science ®Google Scholar
• Diday , E. 1975 . La methode des nuees dynamiques . Revue de Statistique Appliquée , XIX : 19 – 34 .
   Google Scholar
• Roubens , M. 1978 . Pattern classification problems and fuzzy sets . Fuzzy Sets System , 1 : 239 – 253 .
   Google Scholar
• Windham , M. P. 1985 . Numerical classification of proximity data with assignment measures . Journal of Classification , 2 : 157 – 172 .
   Web of Science ®Google Scholar
• Hathaway , R. J. and Bezdek , J. C. 1994 . NERF C-Means: Non-Euclidean relational fuzzy clustering . Pattern Recognition , 27 : 429 – 437 .
   Web of Science ®Google Scholar
• Krishnapuram , R. , Joshi , A. , Nasraoui , O. and Yi , L. 2001 . Low complexity fuzzy relational clustering algorithms for web mining . IEEE Transactions on Fuzzy System , 9 : 595 – 607 .
   Web of Science ®Google Scholar
• Altschul , S. F. , Gish , W. , Miller , W. , Myers , E. and Lipman , D. J. 1990 . Basic local alignment search tool . Journal of Molecular Biology , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Altschul , S. F. , Boguski , M. S. , Gish , W. and Wootton , J. C. 1994 . Issues in searching molecular sequence databases . Nature Genetics , 6 : 119 – 129 .
   PubMed Web of Science ®Google Scholar
• Banerjee , M. , Mitra , S. and Pal , S. K. 1998 . Rough fuzzy MLP: knowledge encoding and classification . IEEE Transactions on Neural Networks , 9 : 1203 – 1216 .
   PubMedGoogle Scholar
• Pearl , L. H. and Taylor , W. R. 1987 . A structural model for the retroviral proteases . Nature , 329 : 351 – 354 .
   PubMed Web of Science ®Google Scholar
• Miller , M. , Schneider , J. , Sathayanarayana , B. K. , Toth , M. V. , Marshall , G. R. , Clawson , L. , Selk , L. , Kent , S. B.H. and Wlodawer , A. 1989 . Structure of complex of synthetic HIV-1 protease with substrate-based inhibitor at 2.3 Å resolution . Science , 246 : 1149 – 1152 .
   PubMed Web of Science ®Google Scholar
• Chou , K. C. 1993 . Vectorised sequence-coupling model for predicting HIV protease cleavage sites in proteins . Journal of Biological Chemistry , 268 : 16938 – 16948 .
   PubMed Web of Science ®Google Scholar
• Barre-Sinoussi , F. , Chermann , J. C. , Rey , F. , Nugeyre , M. T. , Chamaret , S. , Gruest , J. , Dauguet , C. , Axler-Blin , C. , Vezinet-Brun , F. , Rouzioux , C. , Rozenbaum , W. and Montagnier , L. 1983 . Isolation of a T-lymphotropic retrovirus from a patient at risk for Acquired Immune Deficiency Syndrome (AIDS) . Science , 220 : 868 – 871 .
   PubMed Web of Science ®Google Scholar
• Chou , K. C. 1996 . Prediction of human immunodeficiency virus protease cleavage sites in proteins . Analytical Biochemistry , 233 : 1 – 14 .
   PubMed Web of Science ®Google Scholar