-
1
-
-
33646358251
-
Minimotif Miner: a tool for investigating protein function
-
Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR. Minimotif Miner: a tool for investigating protein function. Nat. Methods 2006, 3:175-177.
-
(2006)
Nat. Methods
, vol.3
, pp. 175-177
-
-
Balla, S.1
Thapar, V.2
Verma, S.3
Luong, T.4
Faghri, T.5
Huang, C.H.6
Rajasekaran, S.7
del Campo, J.J.8
Shinn, J.H.9
Mohler, W.A.10
Maciejewski, M.W.11
Gryk, M.R.12
Piccirillo, B.13
Schiller, S.R.14
Schiller, M.R.15
-
2
-
-
0022419375
-
Aromatic-aromatic interaction: a mechanism of protein structure stabilization
-
Burley SK, Petsko GA. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 1985, 229:23-28.
-
(1985)
Science
, vol.229
, pp. 23-28
-
-
Burley, S.K.1
Petsko, G.A.2
-
3
-
-
36749037699
-
Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
-
Cheng Y, Oldfield CJ, Meng J, Romero P, Uversky VN, Dunker AK. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 2007, 46:13468-13477.
-
(2007)
Biochemistry
, vol.46
, pp. 13468-13477
-
-
Cheng, Y.1
Oldfield, C.J.2
Meng, J.3
Romero, P.4
Uversky, V.N.5
Dunker, A.K.6
-
4
-
-
33746812318
-
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
-
Davey NE, Shields DC, Edwards RJ. SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res. 2006, 34:3546-3554.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3546-3554
-
-
Davey, N.E.1
Shields, D.C.2
Edwards, R.J.3
-
5
-
-
0037188377
-
Intrinsic disorder and protein function
-
Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002a, 41:6573-6582.
-
(2002)
Biochemistry
, vol.41
, pp. 6573-6582
-
-
Dunker, A.K.1
Brown, C.J.2
Lawson, J.D.3
Iakoucheva, L.M.4
Obradovic, Z.5
-
6
-
-
0036402827
-
Identification and functions of usefully disordered proteins
-
Dunker AK, Brown CJ, Obradovic Z. Identification and functions of usefully disordered proteins. Adv. Protein Chem. 2002b, 62:25-49.
-
(2002)
Adv. Protein Chem.
, vol.62
, pp. 25-49
-
-
Dunker, A.K.1
Brown, C.J.2
Obradovic, Z.3
-
7
-
-
27144464910
-
Flexible nets. The roles of intrinsic disorder in protein interaction networks
-
Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN. Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J. 2005, 272:5129-5148.
-
(2005)
FEBS J.
, vol.272
, pp. 5129-5148
-
-
Dunker, A.K.1
Cortese, M.S.2
Romero, P.3
Iakoucheva, L.M.4
Uversky, V.N.5
-
9
-
-
52249085709
-
The unfoldomics decade: an update on intrinsically disordered proteins
-
Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 2008a, 9(Suppl 2):S1.
-
(2008)
BMC Genomics
, vol.9
, Issue.SUPPL 2
-
-
Dunker, A.K.1
Oldfield, C.J.2
Meng, J.3
Romero, P.4
Yang, J.Y.5
Chen, J.W.6
Vacic, V.7
Obradovic, Z.8
Uversky, V.N.9
-
10
-
-
57049095821
-
Function and structure of inherently disordered proteins
-
Dunker AK, Silman I, Uversky VN, Sussman JL. Function and structure of inherently disordered proteins. Curr. Opin. Struct. Biol. 2008b, 18:756-764.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 756-764
-
-
Dunker, A.K.1
Silman, I.2
Uversky, V.N.3
Sussman, J.L.4
-
11
-
-
40949105259
-
Signal transduction via unstructured protein conduits
-
Dunker AK, Uversky VN. Signal transduction via unstructured protein conduits. Nat. Chem. Biol. 2008, 4:229-230.
-
(2008)
Nat. Chem. Biol.
, vol.4
, pp. 229-230
-
-
Dunker, A.K.1
Uversky, V.N.2
-
12
-
-
0036468397
-
Coupling of folding and binding for unstructured proteins
-
Dyson HJ, Wright PE. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 2002a, 12:54-60.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 54-60
-
-
Dyson, H.J.1
Wright, P.E.2
-
13
-
-
0036400715
-
Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance
-
Dyson HJ, Wright PE. Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. Adv. Protein Chem. 2002b, 62:311-340.
-
(2002)
Adv. Protein Chem.
, vol.62
, pp. 311-340
-
-
Dyson, H.J.1
Wright, P.E.2
-
14
-
-
14644435825
-
Intrinsically unstructured proteins and their functions
-
Dyson HJ, Wright PE. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 2005, 6:197-208.
-
(2005)
Nat. Rev. Mol. Cell Biol.
, vol.6
, pp. 197-208
-
-
Dyson, H.J.1
Wright, P.E.2
-
15
-
-
33748258328
-
A practical overview of protein disorder prediction methods
-
Ferron F, Longhi S, Canard B, Karlin D. A practical overview of protein disorder prediction methods. Proteins 2006, 65:1-14.
-
(2006)
Proteins
, vol.65
, pp. 1-14
-
-
Ferron, F.1
Longhi, S.2
Canard, B.3
Karlin, D.4
-
16
-
-
0037309985
-
Extended disordered proteins: targeting function with less scaffold
-
Gunasekaran K, Tsai CJ, Kumar S, Zanuy D, Nussinov R. Extended disordered proteins: targeting function with less scaffold. Trends Biochem. Sci. 2003, 28:81-85.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 81-85
-
-
Gunasekaran, K.1
Tsai, C.J.2
Kumar, S.3
Zanuy, D.4
Nussinov, R.5
-
17
-
-
68749093787
-
Predicting intrinsic disorder in proteins: an overview
-
He B, Wang K, Liu Y, Xue B, Uversky VN, Dunker AK. Predicting intrinsic disorder in proteins: an overview. Cell Res. 2009, 19:929-949.
-
(2009)
Cell Res.
, vol.19
, pp. 929-949
-
-
He, B.1
Wang, K.2
Liu, Y.3
Xue, B.4
Uversky, V.N.5
Dunker, A.K.6
-
18
-
-
0348015658
-
The Kullback-Leibler distance
-
Kullback S. The Kullback-Leibler distance. Am. Stat. 1987, 41:340-341.
-
(1987)
Am. Stat.
, vol.41
, pp. 340-341
-
-
Kullback, S.1
-
19
-
-
33847200077
-
Intrinsic disorder in the Protein Data Bank
-
Le Gall T, Romero PR, Cortese MS, Uversky VN, Dunker AK. Intrinsic disorder in the Protein Data Bank. J. Biomol. Struct. Dyn. 2007, 24:325-342.
-
(2007)
J. Biomol. Struct. Dyn.
, vol.24
, pp. 325-342
-
-
Le Gall, T.1
Romero, P.R.2
Cortese, M.S.3
Uversky, V.N.4
Dunker, A.K.5
-
20
-
-
0037303648
-
A structurally disordered region at the C terminus of capsid plays essential roles in multimerization and membrane binding of the gag protein of human immunodeficiency virus type 1
-
Liang C, Hu J, Whitney JB, Kleiman L, Wainberg MA. A structurally disordered region at the C terminus of capsid plays essential roles in multimerization and membrane binding of the gag protein of human immunodeficiency virus type 1. J. Virol. 2003, 77:1772-1783.
-
(2003)
J. Virol.
, vol.77
, pp. 1772-1783
-
-
Liang, C.1
Hu, J.2
Whitney, J.B.3
Kleiman, L.4
Wainberg, M.A.5
-
21
-
-
55949103501
-
Past and future perspectives of synthetic peptide libraries
-
Marasco D, Perretta G, Sabatella M, Ruvo M. Past and future perspectives of synthetic peptide libraries. Curr. Protein Pept. Sci. 2008, 9:447-467.
-
(2008)
Curr. Protein Pept. Sci.
, vol.9
, pp. 447-467
-
-
Marasco, D.1
Perretta, G.2
Sabatella, M.3
Ruvo, M.4
-
22
-
-
33744829805
-
Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation
-
Minezaki Y, Homma K, Kinjo AR, Nishikawa K. Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J. Mol. Biol. 2006, 359:1137-1149.
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 1137-1149
-
-
Minezaki, Y.1
Homma, K.2
Kinjo, A.R.3
Nishikawa, K.4
-
23
-
-
33748456399
-
Analysis of molecular recognition features (MoRFs)
-
Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN. Analysis of molecular recognition features (MoRFs). J. Mol. Biol. 2006, 362:1043-1059.
-
(2006)
J. Mol. Biol.
, vol.362
, pp. 1043-1059
-
-
Mohan, A.1
Oldfield, C.J.2
Radivojac, P.3
Vacic, V.4
Cortese, M.S.5
Dunker, A.K.6
Uversky, V.N.7
-
24
-
-
0242267500
-
Predicting intrinsic disorder from amino acid sequence
-
Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK. Predicting intrinsic disorder from amino acid sequence. Proteins 2003, 53(Suppl 6):566-572.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL 6
, pp. 566-572
-
-
Obradovic, Z.1
Peng, K.2
Vucetic, S.3
Radivojac, P.4
Brown, C.J.5
Dunker, A.K.6
-
25
-
-
30344485673
-
Exploiting heterogeneous sequence properties improves prediction of protein disorder
-
Obradovic Z, Peng K, Vucetic S, Radivojac P, Dunker AK. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 2005, 61(Suppl 7):176-182.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL 7
, pp. 176-182
-
-
Obradovic, Z.1
Peng, K.2
Vucetic, S.3
Radivojac, P.4
Dunker, A.K.5
-
26
-
-
13644257647
-
Comparing and combining predictors of mostly disordered proteins
-
Oldfield CJ, Cheng Y, Cortese MS, Brown CJ, Uversky VN, Dunker AK. Comparing and combining predictors of mostly disordered proteins. Biochemistry 2005a, 44:1989-2000.
-
(2005)
Biochemistry
, vol.44
, pp. 1989-2000
-
-
Oldfield, C.J.1
Cheng, Y.2
Cortese, M.S.3
Brown, C.J.4
Uversky, V.N.5
Dunker, A.K.6
-
27
-
-
24944546549
-
Coupled folding and binding with alpha-helix-forming molecular recognition elements
-
Oldfield CJ, Cheng Y, Cortese MS, Romero P, Uversky VN, Dunker AK. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 2005b, 44:12454-12470.
-
(2005)
Biochemistry
, vol.44
, pp. 12454-12470
-
-
Oldfield, C.J.1
Cheng, Y.2
Cortese, M.S.3
Romero, P.4
Uversky, V.N.5
Dunker, A.K.6
-
28
-
-
33745289067
-
Length-dependent prediction of protein intrinsic disorder
-
Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 2006, 7:208.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 208
-
-
Peng, K.1
Radivojac, P.2
Vucetic, S.3
Dunker, A.K.4
Obradovic, Z.5
-
29
-
-
14544299774
-
Optimizing long intrinsic disorder predictors with protein evolutionary information
-
Peng K, Vucetic S, Radivojac P, Brown CJ, Dunker AK, Obradovic Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J Bioinform Comput Biol 2005, 3:35-60.
-
(2005)
J Bioinform Comput Biol
, vol.3
, pp. 35-60
-
-
Peng, K.1
Vucetic, S.2
Radivojac, P.3
Brown, C.J.4
Dunker, A.K.5
Obradovic, Z.6
-
30
-
-
0042622252
-
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
-
Puntervoll P, Linding R, Gemund C. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 2003, 31:3625-3630.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3625-3630
-
-
Puntervoll, P.1
Linding, R.2
Gemund, C.3
-
31
-
-
33847795359
-
Intrinsic disorder and functional proteomics
-
Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Intrinsic disorder and functional proteomics. Biophys. J. 2007, 92:1439-1456.
-
(2007)
Biophys. J.
, vol.92
, pp. 1439-1456
-
-
Radivojac, P.1
Iakoucheva, L.M.2
Oldfield, C.J.3
Obradovic, Z.4
Uversky, V.N.5
Dunker, A.K.6
-
32
-
-
0022555901
-
Study of protein dynamics by X-ray diffraction
-
Ringe D, Petsko GA. Study of protein dynamics by X-ray diffraction. Methods Enzymol. 1986, 131:389-433.
-
(1986)
Methods Enzymol.
, vol.131
, pp. 389-433
-
-
Ringe, D.1
Petsko, G.A.2
-
33
-
-
0030691703
-
Identifying Disordered regions in proteins from amino acid sequences
-
Romero P, Obradovic Z, Kissinger CR, Villafranca JE, Dunker AK. Identifying Disordered regions in proteins from amino acid sequences. IEEE Int. Conf. Neural Networks 1997, 1:90-95.
-
(1997)
IEEE Int. Conf. Neural Networks
, vol.1
, pp. 90-95
-
-
Romero, P.1
Obradovic, Z.2
Kissinger, C.R.3
Villafranca, J.E.4
Dunker, A.K.5
-
34
-
-
0035188314
-
Sequence complexity of disordered protein
-
Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, Dunker AK. Sequence complexity of disordered protein. Proteins 2001, 42:38-48.
-
(2001)
Proteins
, vol.42
, pp. 38-48
-
-
Romero, P.1
Obradovic, Z.2
Li, X.3
Garner, E.C.4
Brown, C.J.5
Dunker, A.K.6
-
35
-
-
33846099868
-
DisProt: the Database of Disordered Proteins
-
Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK. DisProt: the Database of Disordered Proteins. Nucleic Acids Res. 2007, 35:D786-D793.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Sickmeier, M.1
Hamilton, J.A.2
LeGall, T.3
Vacic, V.4
Cortese, M.S.5
Tantos, A.6
Szabo, B.7
Tompa, P.8
Chen, J.9
Uversky, V.N.10
Obradovic, Z.11
Dunker, A.K.12
-
36
-
-
1642533607
-
The functional benefits of protein disorder
-
Tompa P. The functional benefits of protein disorder. Journal of Molecular Structure-Theochem 2003, 666:361-371.
-
(2003)
Journal of Molecular Structure-Theochem
, vol.666
, pp. 361-371
-
-
Tompa, P.1
-
37
-
-
57149085681
-
Biochemistry. Controlled chaos
-
Uversky VN, Dunker AK. Biochemistry. Controlled chaos. Science 2008, 322:1340-1341.
-
(2008)
Science
, vol.322
, pp. 1340-1341
-
-
Uversky, V.N.1
Dunker, A.K.2
-
38
-
-
0034669882
-
Why are " natively unfolded" proteins unstructured under physiologic conditions?
-
Uversky VN, Gillespie JR, Fink AL. Why are " natively unfolded" proteins unstructured under physiologic conditions? Proteins 2000, 41:415-427.
-
(2000)
Proteins
, vol.41
, pp. 415-427
-
-
Uversky, V.N.1
Gillespie, J.R.2
Fink, A.L.3
-
39
-
-
25144472591
-
Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling
-
Uversky VN, Oldfield CJ, Dunker AK. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit. 2005, 18:343-384.
-
(2005)
J. Mol. Recognit.
, vol.18
, pp. 343-384
-
-
Uversky, V.N.1
Oldfield, C.J.2
Dunker, A.K.3
-
40
-
-
34250815165
-
Characterization of molecular recognition features, MoRFs, and their binding partners
-
Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK. Characterization of molecular recognition features, MoRFs, and their binding partners. J. Proteome Res. 2007a, 6:2351-2366.
-
(2007)
J. Proteome Res.
, vol.6
, pp. 2351-2366
-
-
Vacic, V.1
Oldfield, C.J.2
Mohan, A.3
Radivojac, P.4
Cortese, M.S.5
Uversky, V.N.6
Dunker, A.K.7
-
41
-
-
34447539760
-
Composition Profiler: a tool for discovery and visualization of amino acid composition differences
-
Vacic V, Uversky VN, Dunker AK, Lonardi S. Composition Profiler: a tool for discovery and visualization of amino acid composition differences. Bmc Bioinformatics 2007b, 8:211.
-
(2007)
Bmc Bioinformatics
, vol.8
, pp. 211
-
-
Vacic, V.1
Uversky, V.N.2
Dunker, A.K.3
Lonardi, S.4
-
42
-
-
0027509952
-
A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein
-
Vershon AK, Johnson AD. A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein. Cell 1993, 72:105-112.
-
(1993)
Cell
, vol.72
, pp. 105-112
-
-
Vershon, A.K.1
Johnson, A.D.2
-
43
-
-
0032749078
-
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
-
Wright PE, Dyson HJ. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 1999, 293:321-331.
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
45
-
-
76849087968
-
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
-
Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim. Biophys. Acta 2010, 1804:996-1010.
-
(2010)
Biochim. Biophys. Acta
, vol.1804
, pp. 996-1010
-
-
Xue, B.1
Dunbrack, R.L.2
Williams, R.W.3
Dunker, A.K.4
Uversky, V.N.5
-
46
-
-
72949087534
-
Analysis of structured and intrinsically disordered regions of transmembrane proteins
-
Xue B, Li L, Meroueh SO, Uversky VN, Dunker AK. Analysis of structured and intrinsically disordered regions of transmembrane proteins. Mol Biosyst 2009a, 5:1688-1702.
-
(2009)
Mol Biosyst
, vol.5
, pp. 1688-1702
-
-
Xue, B.1
Li, L.2
Meroueh, S.O.3
Uversky, V.N.4
Dunker, A.K.5
-
47
-
-
67349162535
-
CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions
-
Xue B, Oldfield CJ, Dunker AK, Uversky VN. CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions. FEBS Lett. 2009b, 583:1469-1474.
-
(2009)
FEBS Lett.
, vol.583
, pp. 1469-1474
-
-
Xue, B.1
Oldfield, C.J.2
Dunker, A.K.3
Uversky, V.N.4
|