From Protein Structure to Function with Bioinformatics.pdf

12 Prediction of Protein Function from Theoretical Models 317Tatusov RL, Fedorova ND, Jackson JD, et al. (2003) The COG database: an updated versionincludes eukaryotes. BMC Bioinformatics 4:41Tress M, Bujnicki JM, Valencia A (2008) Integrating structures, functions, and interactions. In:Bujnicki JM (ed.), Prediction of Protein Structures, Functions and Interactions. Wiley.Tress ML, Martelli PL, Frankish A, et al. (2007) The implications of alternative splicing in theENCODE protein complement. Proc Natl Acad Sci USA 104:5495–5500van Gunsteren W (1996) Biomolecular Simulations: The GROMOS96 Manual and User Guide.Biomos : GroningenWallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci12:1073–1086Wallner B, Elofsson A (2006) Identification of correct regions in protein models using structural,alignment, and consensus information. Protein Sci 15:900–913Wang P, Yan B, Guo JT, et al. (2005) Structural genomics analysis of alternative splicing andapplication to isoform structure modeling. Proc Natl Acad Sci USA 102:18920–18925Xu LZ, Sanchez R, Sali A, et al. (1996) Ligand specificity of brain lipid-binding protein. J BiolChem 271:24711–24719Yooseph S, Sutton G, Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition:expanding the universe of protein families. PLoS Biol 5:e16