From Protein Structure to Function with Bioinformatics.pdf
From Protein Structure to Function with Bioinformatics.pdf
From Protein Structure to Function with Bioinformatics.pdf
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138 P. TompaMark WY, Liao JC, Lu Y, et al. (2005) Characterization of segments from the central region ofBRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNAinteractions? J Mol Biol 345:275–287Minezaki Y, Homma K, Kinjo AR, et al. (2006) Human transcription fac<strong>to</strong>rs contain a high fractionof intrinsically disordered regions essential for transcriptional regulation. J Mol Biol359:1137–1149Mohan A, Oldfield CJ, Radivojac P, et al. (2006) Analysis of molecular recognition features(MoRFs). J Mol Biol 362:1043–1059Mukhopadhyay R, Hoh JH (2001) AFM force measurements on microtubule-associated proteins:the projection domain exerts a long-range repulsive force. FEBS Lett 505:374–378.Neduva V, Russell RB (2005) Linear motifs: evolutionary interaction switches. FEBS Lett579:3342–3345Neduva V, Russell RB (2006) DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res34:W350–355Neduva V, Linding R, Su-Angrand I, et al. (2005) Systematic discovery of new recognition peptidesmediating protein interaction networks. PLoS Biol 3:e405Ng KP, Potikyan G, Savene RO, et al. (2007) Multiple aromatic side chains <strong>with</strong>in a disorderedstructure are critical for transcription and transforming activity of EWS family oncoproteins.Proc Natl Acad Sci USA 104:479–484Obenauer JC, Cantley LC, Yaffe MB (2003) Scansite 2.0: Proteome-wide prediction of cell signalinginteractions using short sequence motifs. Nucleic Acids Res 31:3635–3641Olashaw N, Bagui TK, Pledger WJ (2004) Cell cycle control: a complex issue. Cell Cycle3:263–264Oldfield CJ, Cheng Y, Cortese MS, et al. (2005a) Comparing and combining predic<strong>to</strong>rs of mostlydisordered proteins. Biochemistry 44:1989–2000Oldfield CJ, Cheng Y, Cortese MS, et al. (2005b) Coupled folding and binding <strong>with</strong> alpha-helixformingmolecular recognition elements. Biochemistry 44:12454–12470Olson KE, Narayanaswami P, Vise PD, et al. (2005) Secondary structure and dynamics of anintrinsically unstructured linker domain. J Biomol Struct Dyn 23:113–124Patil A, Nakamura H (2006) Disordered domains and high surface charge confer hubs <strong>with</strong> theability <strong>to</strong> interact <strong>with</strong> multiple proteins in interaction networks. FEBS Lett580:2041–2045Pawson T, Nash P (2003) Assembly of cell regula<strong>to</strong>ry systems through protein interactiondomains. Science 300:445–452Peng K, Radivojac P, Vucetic S, et al. (2006) Length-dependent prediction of protein intrinsic disorder.BMC <strong>Bioinformatics</strong> 7:208Pierce MM, Baxa U, Steven AC, et al. (2005) Is the prion domain of soluble Ure2p unstructured?Biochemistry 44:321–328Pontius BW (1993) Close encounters: why unstructured, polymeric domains can increase rates ofspecific macromolecular association. Trends Biochem Sci 18:181–186.Prilusky J, Felder CE, Zeev-Ben-Mordehai T, et al. (2005) FoldIndex: a simple <strong>to</strong>ol <strong>to</strong> predictwhether a given protein sequence is intrinsically unfolded. <strong>Bioinformatics</strong> 21:3435–3438Prusiner SB (1998) Prions. Proc Natl Acad Sci USA 95:13363–13383Puntervoll P, Linding R, Gemund C, et al. (2003) ELM server: a new resource for investigatingshort functional sites in modular eukaryotic proteins. Nucleic Acids Res 31:3625–3630Radhakrishnan I, Perez-Alvarado GC, Dyson HJ, et al. (1998) Conformational preferences in theSer133-phosphorylated and non-phosphorylated forms of the kinase inducible transactivationdomain of CREB. FEBS Lett 430:317–322Radivojac P, Vucetic S, O’Connor TR, et al. (2006) Calmodulin signaling: analysis and predictionof a disorder-dependent molecular recognition. <strong>Protein</strong>s 63:398–410Romero P, Obradovic Z, Kissinger CR, et al. (1998) Thousands of proteins likely <strong>to</strong> have longdisordered regions. Pac Symp Biocomputing 3:437–448Romero P, Obradovic Z, Dunker AK (1999) Folding minimal sequences: the lower bound forsequence complexity of globular proteins. FEBS Lett 462:363–367