References
- Albert, R., Jeong, H., and Barabasi, A.L. (2000). Error and attack tolerance of complex networks. Nature 406, 378-382 https://doi.org/10.1038/35019019
- Albert, R. and Othmer, H.G., (2003). The topology of the regulat- ory interactions predicts the expression pattern of the seg- ment polarity genes in Drosophila melanogaster. J.Theor. Biol. 223, 1-18 https://doi.org/10.1016/S0022-5193(03)00035-3
- Albert, R. and Baraba'si, A.-L (2002). Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47-97 https://doi.org/10.1103/RevModPhys.74.47
- Batagelj, V. and Mrvar, A. (2001). Pajek-analysis and visualization of large networks. LNCS 2265, 477-478
- Bolser, D.M. and Park, J. (2003). Biological Network Evolution Hypothesis Applied to Protein Structural Interactome. Genomics & Informatics 7-19
- Bolser, D., Panos, D, Harrington, R., Park, J., and Schroeder, M., (2003). Visualisation and Graph- theoretic Analysis of a Large-scale Protein Structural Interactome., BMC Bioinformatics 445, 1471-2105
- Bray, D. (1995). Protein molecules as computational elements in living cells. Nature 376, 307-312 https://doi.org/10.1038/376307a0
- Caffrey, D.R., Somaroo, S., Hughes, J.D., Mintseris, J., and Huang, E.S. (2004). Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science 13, 190-202 https://doi.org/10.1110/ps.03323604
- Chia, J.M, and Kolatkar, P.R. (2004). Implications for domain fusn protein-protein interactions based on structuralio information. BMC Bioinformatics 26, 161 (Epub ahead of print)
- Chothia, C. and Janin, J. (1975). Principles of protein-protein recognition. Nature 256, 705-708 https://doi.org/10.1038/256705a0
- Chothia, C. (1976). The nature of the accessible and buried surfaces in proteins. J.MoI.BioI. 105, 1-14 https://doi.org/10.1016/0022-2836(76)90191-1
- Darwin, C. (1859). On the origins of species, London, http://pages.britishlibrary.net/charles.darwin/texts/origin1859/origin_fm.html
- Doolittle, R.F., Feng, D.F., Tsang, S., Cho, G., and Little, E., (1996). Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science 27-1, 470-477
- Enright, A.J., Iliopoulos, I., Kyrpides, N.C., and Ouzounis, C.A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90 https://doi.org/10.1038/47056
- Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome, Y. Proc. Natl. Acad. Sci. USA 98, 4569-4574. Epub https://doi.org/10.1073/pnas.061034498
- Jones, S. and Thornton, J.M. (1997). Analysis of Protein-protein interaction sites using surface patches. J.MoI.Biol. 272, 121-132 https://doi.org/10.1006/jmbi.1997.1234
- Jones, S. and Thornton, J.M. (1997). Principle of protein- protein interactions. Proc. Natl. Acad. Sci. USA 93, 13-20 https://doi.org/10.1073/pnas.93.1.13
- Jones, S., Marin, A., and Thornton, J.M. (2000). Protein domain interfaces: characterization and comparison with oligomeric protein interfaces. Protein Engineering 13, 77-82 https://doi.org/10.1093/protein/13.2.77
- Ju, B.H., Park, B., Park J.H., and Han K. (2003). Visualization and analysis of protein interactions. Bioinformatics 19, 317-318 https://doi.org/10.1093/bioinformatics/19.2.317
- Gagneur, J, Krause, R., Bouwmeester, T., and Casari, G. (2004). Modular decomposition of protein-protein interaction networks. Genome Biol. 5, R57. Epub https://doi.org/10.1186/gb-2004-5-8-r57
- Gardiner, K., Davisson M.T., and Crnic, L.S. (2004). Building protein interaction maps for Down's syndrome. Brief Funct Genomic Proteomic 3, 142-156 https://doi.org/10.1093/bfgp/3.2.142
-
Lu, H., Zhu, X., Liu, H., Skoger
$\phi$ , G., Zang, L., Zang, Y., Cai, L., Zhao, Y., Sun, S., Xu, J., Bu, D., and Chen, R. (2004). The interactome as a tree-an attempt to visualize the protein-protein interaction network in yeast. Nucleic Acids Research 32, 4804-4811 https://doi.org/10.1093/nar/gkh814 - Iragne, F., Nikolski, M., Mathieu, B., Auber, D., and Sherman D. (2004). ProViz: Protein Interaction Visualization and Exploration. Bioinformatics (Epub ahead of print)
- Jeong, H., Mason, S.P., Barabasi, A.L., and Oltvai, Z.N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42 https://doi.org/10.1038/35075138
- Kim, W., Bolser, D.M., and Park, J., (2004). Large scale co-evolution analysis of Protein Structural Interlogues using the global Protein Structural Interactome Map (PSIMAP). Bioinformatics 20, 1138-1150 https://doi.org/10.1093/bioinformatics/bth053
- Kim, H., Park, J., and Han, K, (2003). Predicting Protein Interactions in Human by Homologous Interactions in Yeast. Lecture Notes in Computer Science 2637, 159-165 https://doi.org/10.1007/3-540-36175-8_16
- Lappe, M., Park, J., Niggemann, 0., and Holm, L. (2001). Generating protein interaction maps from incomplete data: application to Fold assignment. Bioinformatics VoI.17 SuppI.1, S149-S156 https://doi.org/10.1093/bioinformatics/17.2.149
- Lehner, B. and Fraser, F. (2004). A first-draft human protein-interaction map. Genome Biology 5:R63 doi:10.1186/ gb-2004-5-9-r63
- Lawrence, M.C. and Colman, P.M. (1993). Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950 https://doi.org/10.1006/jmbi.1993.1648
- Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 https://doi.org/10.1126/science.285.5428.751
- Miller, S., Janin, J., Lesk, A.M., and Chotia, C. (1987). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656 https://doi.org/10.1016/0022-2836(87)90038-6
- Moon, H.S., Bhak, J., Lee, K.H., and Lee, D. (2005). Architecture of Basic Building Blocks in Protein and Domain Structural Interaction Networks. Bioinformatics (in press)
- Ng, S.K. and Tan, S.H. (2004). Discovering protein-protein interactions. J. Bioinform Comput. Biol. 1, 711-741 https://doi.org/10.1142/S0219720004000600
- Park, J., Dietmann, S., Heger, A., and Holm, L. (2000). Estimating the significance of sequence order in protein secondary structure prediction. Bioinformatics 16, 978-987 https://doi.org/10.1093/bioinformatics/16.11.978
- Park, J. and Bolser, D., (2001). Conservation of protein interaction network in evolution. Genome Informatics 12, 135-140
- Park, J., Lappe, M., and Teichmann, S.A. (2001). Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 30, 307, 929-938
- Poupon, A. (2004). Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Curr. Opio. Stru. Biol. 14, 1-9 https://doi.org/10.1016/j.sbi.2004.01.007
- Promislow, D.E. (2004). Protein networks, pleiotropy and the evolution of senescence. Proc. R. Soc. Lond. B. Biol. Sci. 271, 1225-1234 https://doi.org/10.1098/rspb.2004.2732
- Raicu V., Jansma D.B., Miller R.J., and Friesen J.D. (2004). Protein interaction quantified in vivo by spectrally resolved fluorescence resonance energy transfer. Biochem J. Sep 7;Pt. (Epub ahead of print)
- Richard, F.M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14 https://doi.org/10.1016/0022-2836(74)90570-1
- Richards, F.M. (1977). Area, volumes, Packing and protein structures, Ann. Rev. Biophys. Bioeng. 6, 151-176 https://doi.org/10.1146/annurev.bb.06.060177.001055
- Varshney A., Brooks, F., and Richardson, D. (1995). Defining, Computing, and Visualizing Molecular Interfaces. Proceedings IEEE Visualization 95, 36-43
- Sanchez, C., Lachaize, C., Janody, F., Bellon, B., Roder, L, Euzenat, J., Rechenmann, F., and Jacq, B. (1999). Grasping at molecular interactions and genetic networksin Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res. 27, 89-94 https://doi.org/10.1093/nar/27.1.89
- Schof, J.W. (1993). Microfossils of the EarIy Archean Apex Chert: New Evidence of the Antiquity of life. Science 260, 640-646 https://doi.org/10.1126/science.260.5108.640
- Searls, D.B. (1993). The Computational Linguistics of Biological Sequences, In Artificial Intelligence and Molecular Biology, L. Hunter, ed. (AAAI Press) PP.47-120
- Uetz, P., Giot, L, Cagney, G., Mansfield, T.A., Judson, RS., Knight, J.R., Lockshon, D., Narayan, V., Shnivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J.M. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 https://doi.org/10.1038/35001009
- Walhout, A.J., Boulton, S.J., and Vidal, M. (2000). Yeast two hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17, 88-94 https://doi.org/10.1002/1097-0061(20000630)17:2<88::AID-YEA20>3.0.CO;2-Y