PAPERS FOR DISCUSSION

• Tatusov RL, Koonin EV, Lipman DJ.  A genomic perspective on protein families. Science. 1997 Oct 24;278(5338):631-7. Review.
• Basic
• Tatusov_COG_1997_Science_278(5338):631.pdf
• Kunin V, Cases I, Enright AJ, de Lorenzo V, Ouzounis CA. Myriads of protein families, and still counting. Genome Biol. 2003;4(2):401.
• General
• Kunin_ProtFams_2003_GenomeBio_4(2):401.pdf
• Devos D, Valencia A. Practical limits of function prediction. Proteins. 2000 Oct 1;41(1):98-107.
• Basic
• Devos_PractLimits_2000_Proteins_41(1):98.pdf
• von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B.  STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003 Jan 1;31(1):258-61.
• Advanced
• vonMering_STRING_2003_NAR_31(1):258.pdf
• von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002 May 23;417(6887):399-403.
• Advanced
• vonMering_InterNetw_2002_Nature_417(6687):339.pdf
• Blaschke C, Hirschman L and Valencia A. (2002) Information extraction in Molecular Biology, Briefings in Bioinformatics 3: 154-165.
• General
• Blaschke_InformExtract_2002_BriefBioinfo_3():154.pdf.
• Liisa Holm and Chris Sander. Mapping the Protein Universe (1998) 273 (5275) p595
• General - A review of 3D structural comparison.
• holm96.pdf.
• A.N. Lupas, C.P. Ponting, R.B. Russell On the Evolution of Protein Folds: Are similar motifs in different protein folds the result of convergence, insertion or relics of an ancient peptide world? J. Struct. Biol., 134,191-203, 2001 .
• Advanced
• Lupas01.pdf