Bio-medical Ontologies Maintenance and Change Management

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342 M.T. Hoque, M. Chetty, and A. Sattar 77. Patton, A.L., Punch, W.F., Goodman, E.D.: A Standard GA approach to Native Protein Conformation Prediction. In: 6th International Conference on Genetic Algorithms, pp. 574–581 (1995) 78. Krasnogor, N., Hart, W.E., Smith, J., Pelta, D.A.: Protein Structure Prediction With Evolutionary Algorithms. In: Genetic and Evolutionary Computation Conference, GECCO 1999 (1999) 79. Bornberg-Bauer, E.: Chain Growth Algorithms for HP-Type Lattice Proteins. In: RECOMB, Santa Fe, NM, USA (1997) 80. Hoque, M.T., Chetty, M., Dooley, L.: A Guided Genetic Algorithm for Protein Folding Prediction Using 3D Hydrophobic-Hydrophilic Model. In: Special session in WCCI / IEEE Congress on Evolutionary Computation, CEC (2006) 81. Hoque, M.T., Chetty, M., Dooley, L.S.: A Hybrid Genetic Algorithm for 2D FCC Hydrophobic-Hydrophilic Lattice Model to Predict Protein Folding. In: Sattar, A., Kang, B.-h. (eds.) AI 2006. LNCS(LNAI), vol. 4304, pp. 867–876. Springer, Heidelberg (2006) 82. Hoque, M.T., Chetty, M., Sattar, A.: Protein Folding Prediction in 3D FCC HP Lattice Model Using Genetic Algorithm Bioinformatics special session. In: IEEE Congress on Evolutionary Computation (CEC), Singapore (2007) 83. Yue, K., Dill, K.A.: Sequence-structure relationships in proteins and copolymers. Phys. Rev. E 48, 2267–2278 (1993) 84. Bonneau, R., Strauss, C., Baker, D.: Improving the Performance of Rosetta Using Multiple Sequence Alignment Information and Global Measures of Hydrophobic Core. PROTEINS: Structure, Function, and Genetics 43, 1–11 (2001) 85. Toma, L., Toma, S.: Contact interactions methods: A new Algorithm for Protein Folding Simulations. Protein Science 5, 147–153 (1996) 86. Backofen, R., Will, S.: A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models. Kluwer Academic Publishers, Dordrecht (2005) 87. Raghunathan, G., Jernigan, R.L.: Ideal architecture of residue packing and its observation in protein structures. Protein Sci. 10, 2072–2083 (1997) 88. Wikipedia: Cuboctahedron (February 2007), http://en.wikipedia.org/wiki/Cuboctahedron 89. Backofen, R., Will, S., Bornberg-Bauer, E.: Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinformatics 15, 234–242 (1999) 90. Guo, Y.Z., Feng, E.M., Wang, Y.: Exploration of two-dimensional hydrophobic-polar lattice model by combining local search with elastic net algorithm. J. Chem. Phys. 125 (2006) 91. Crippen, G.M.: Prediction of Protein Folding from Amino Acid Sequence over Discrete Conformation Spaces. Biochemistry 30, 4232–4237 (1991) 92. Hoque, M.T., Chetty, M., Sattar, A.: Extended HP model for Protein Structure Prediction. Journal of Computational Biology 16, 1–19 (2007) 93. Jordan, J.K., Kondrashov, F.A., Adzhubei, I.A., Wolf, Y.I., Koonin, E.V., Kondrashov, A.S., Sunyaev, S.: A universal trend of amino acid gain and loss in protein evolution. Letter to Nature 433 (2005) 94. PDB, Protein Data Base (April 2007), http://www.rcsb.org/pdb/
Author Index Apiletti, Daniele 169 Baralis, Elena 169 Bellgard, Matthew 1, 55 Berlingerio, Michele 211 Bonchi, Francesco 211 Brezovan, Marius 71 Brouwer, Rick 281 Bruno, Giulia 169 Cannata, Nicola 13 Chen, Jake Y. 265 Chen, Meifania 281 Chetty, Madhu 317 Cook, Diane J. 237 Corradini, Flavio 13 Curcio, Michele 211 Dan Burdescu, Dumitru 71 De Francesco, Erika 37 Dillon, Tharam S. 1 Di Santo, Giuliana 37 Fernandez, Margarita 295 Ficarra, Elisa 169 Giannotti, Fosca 211 Godínez, Israel Román 187 Haarslev, Volker 143 Hadzic, Maja 281 Holder, Lawrence B. 237 Hoque, Md. Tamjidul 317 Lloyd, Frank 265 López-Yáñez, Itzamá 187 Merelli, Emanuela 13 Palopoli, Luigi 37 Piersigilli, Francesca 13 Rombo, Simona E. 37 Sattar, Abdul 317 Shaban-Nejad, Arash 143 Sidhu, Amandeep S. 1, 55 Stanescu, Liana 71 Streja, Dan 295 Taduri, Shailaja 265 Turini, Franco 211 Villasana, Minaya 295 Vito, Leonardo 13 Yáñez-Márquez, Cornelio 187 You, Chang hun 237
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Amandeep S. Sidhu and Tharam S. Dil
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Amandeep S. Sidhu and Tharam S. Dil
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Preface The molecular biology commu
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Preface VII biomedical systems, and
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X Contents Mining Clinical, Immunol
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2 A.S. Sidhu, M. Bellgard, and T.S.
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Towards Bioinformatics Resourceomes
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2 The New Waves Towards Bioinformat
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2.4 Semantic Web Towards Bioinforma
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A Summary of Genomic Databases: Ove
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Appendix A Summary of Genomic Datab
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Protein Data Integration Problem Am
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Protein Data Integration Problem 57
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Fig. 3. Class Hierarchy of Protein
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72 L. Stanescu, D. Dan Burdescu, an
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Bio-medical Ontologies Maintenance
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TextToOnto (Maedche and Volz 2001)
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Extraction of Constraints from Biol
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Classifying Patterns in Bioinformat
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Mining Clinical, Immunological, and
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Substructure Analysis of Metabolic
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entry compound relation subtype com
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Running Time 4500 4000 3500 3000 25
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6 Conclusion Substructure Analysis
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266 J.Y. Chen, S. Taduri, and F. Ll
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Completing the Total Wellbeing Puzz
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