-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
doi: 10.1093/nar/25.17.3389
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. doi: 10.1093/nar/25.17.3389.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
doi: 10.1093/nar/gkh039
-
Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2004. SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res. 32: D226-D229. doi: 10.1093/nar/gkh039.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
3
-
-
10844225367
-
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
-
Bastolla, U., Porto, M., Roman, H.E., and Vendruscolo, M. 2005. Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58: 22-30.
-
(2005)
Proteins
, vol.58
, pp. 22-30
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
4
-
-
37049161544
-
The energy and entropy of hydration of organic compounds
-
Butler, J.A.V. 1937. The energy and entropy of hydration of organic compounds. Trans. Faraday Soc. 33: 229-236.
-
(1937)
Trans. Faraday Soc
, vol.33
, pp. 229-236
-
-
Butler, J.A.V.1
-
5
-
-
0036495864
-
A fast annealing evolutionary algorithm for global optimization
-
Cai, W. and Shao, X. 2002. A fast annealing evolutionary algorithm for global optimization. J. Comput. Chem. 23: 427-435.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 427-435
-
-
Cai, W.1
Shao, X.2
-
6
-
-
26944481188
-
Interfaces and the driving force of hydrophobic assembly
-
Chandler, D. 2005. Interfaces and the driving force of hydrophobic assembly. Nature 437: 640-647.
-
(2005)
Nature
, vol.437
, pp. 640-647
-
-
Chandler, D.1
-
7
-
-
27944488680
-
Accurate prediction of protein disordered regions by mining protein structure data
-
Cheng, J., Sweredoski, M.J., and Baldi, P. 2005. Accurate prediction of protein disordered regions by mining protein structure data. Data Mining Knowledge Discovery 11: 213-222.
-
(2005)
Data Mining Knowledge Discovery
, vol.11
, pp. 213-222
-
-
Cheng, J.1
Sweredoski, M.J.2
Baldi, P.3
-
8
-
-
0017187836
-
The nature of the accessible and buried surfaces in proteins
-
Chothia, C. 1976. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105: 1-12.
-
(1976)
J. Mol. Biol
, vol.105
, pp. 1-12
-
-
Chothia, C.1
-
9
-
-
0015967881
-
Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins
-
Chou, P.Y. and Fasman, G.D. 1974. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry 13: 211-222.
-
(1974)
Biochemistry
, vol.13
, pp. 211-222
-
-
Chou, P.Y.1
Fasman, G.D.2
-
10
-
-
0026636312
-
Hydrophobicity and structural classes in proteins
-
Cid, H., Bunster, M., Canales, M., and Gazitua, F. 1992. Hydrophobicity and structural classes in proteins. Protein Eng. 5: 373-375.
-
(1992)
Protein Eng
, vol.5
, pp. 373-375
-
-
Cid, H.1
Bunster, M.2
Canales, M.3
Gazitua, F.4
-
11
-
-
18744405418
-
Prediction of unfolded segments in a protein sequence based on amino acid composition
-
Coeytaux, K. and Poupon, A. 2005. Prediction of unfolded segments in a protein sequence based on amino acid composition. Bioinformatics 21: 1891-1900.
-
(2005)
Bioinformatics
, vol.21
, pp. 1891-1900
-
-
Coeytaux, K.1
Poupon, A.2
-
12
-
-
34748889919
-
-
Creighton, T.E. 1993, 2002. Proteins: Structures and molecular properties, 2nd ed. W.H. Freeman Company, New York.
-
Creighton, T.E. 1993, 2002. Proteins: Structures and molecular properties, 2nd ed. W.H. Freeman Company, New York.
-
-
-
-
13
-
-
24044538903
-
IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
-
Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. 2005a. IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21: 3433-3434.
-
(2005)
Bioinformatics
, vol.21
, pp. 3433-3434
-
-
Dosztanyi, Z.1
Csizmok, V.2
Tompa, P.3
Simon, I.4
-
14
-
-
14844342815
-
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
-
Dosztanyi, Z., Csizmok, V., Tompa, P., and Simon, I. 2005b. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol. 347: 827-839.
-
(2005)
J. Mol. Biol
, vol.347
, pp. 827-839
-
-
Dosztanyi, Z.1
Csizmok, V.2
Tompa, P.3
Simon, I.4
-
15
-
-
34247595555
-
Prediction of protein disorder at the domain level
-
Dosztanyi, Z., Sandor, M., Tompa, P., and Simon, I. 2007. Prediction of protein disorder at the domain level. Curr. Protein Pept. Sci. 8: 161-171.
-
(2007)
Curr. Protein Pept. Sci
, vol.8
, pp. 161-171
-
-
Dosztanyi, Z.1
Sandor, M.2
Tompa, P.3
Simon, I.4
-
16
-
-
33749517180
-
Honing the in silico toolkit for detecting protein disorder
-
Esnouf, R.M., Hamer, R., Sussman, J.L., Silman, I., Trudgian, D., Yang, Z.R., and Prilusky, J. 2006. Honing the in silico toolkit for detecting protein disorder. Acta Crystallogr. D Biol. Crystallogr. 62: 1260-1266.
-
(2006)
Acta Crystallogr. D Biol. Crystallogr
, vol.62
, pp. 1260-1266
-
-
Esnouf, R.M.1
Hamer, R.2
Sussman, J.L.3
Silman, I.4
Trudgian, D.5
Yang, Z.R.6
Prilusky, J.7
-
17
-
-
33748258328
-
A practical overview of protein disorder prediction methods
-
Ferron, F., Longhi, S., Canard, B., and Karlin, D. 2006. A practical overview of protein disorder prediction methods. Proteins 65: 1-14.
-
(2006)
Proteins
, vol.65
, pp. 1-14
-
-
Ferron, F.1
Longhi, S.2
Canard, B.3
Karlin, D.4
-
18
-
-
33751381791
-
FoldUnfold: Web server for the prediction of disordered regions in protein chain
-
Galzitskaya, O.V., Garbuzynskiy, S.O., and Lobanov, M.Y. 2006a. FoldUnfold: Web server for the prediction of disordered regions in protein chain. Bioinformatics 22: 2948-2949.
-
(2006)
Bioinformatics
, vol.22
, pp. 2948-2949
-
-
Galzitskaya, O.V.1
Garbuzynskiy, S.O.2
Lobanov, M.Y.3
-
19
-
-
33845990277
-
Prediction of amyloidogenic and disordered regions in protein chains
-
doi: 10.1371/journal.pcbi.0020177
-
Galzitskaya, O.V., Garbuzynskiy, S.O., and Lobanov, M.Y. 2006b. Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput. Biol. 2: e177. doi: 10.1371/journal.pcbi.0020177.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Galzitskaya, O.V.1
Garbuzynskiy, S.O.2
Lobanov, M.Y.3
-
20
-
-
0001969211
-
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
-
Gribskov, M. and Robinson, N.L. 1996. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20: 25-33.
-
(1996)
Comput. Chem
, vol.20
, pp. 25-33
-
-
Gribskov, M.1
Robinson, N.L.2
-
21
-
-
0021977590
-
Amino acid side-chain partition energies and distribution of residues in soluble proteins
-
Guy, H.R. 1985. Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys. J. 47: 61-70.
-
(1985)
Biophys. J
, vol.47
, pp. 61-70
-
-
Guy, H.R.1
-
22
-
-
33846594201
-
Predicting disordered regions in proteins based on decision trees of reduced amino acid composition
-
Han, P., Zhang, X., Norton, R.S., and Feng, Z.P. 2006. Predicting disordered regions in proteins based on decision trees of reduced amino acid composition. J. Comput. Biol. 13: 1723-1734.
-
(2006)
J. Comput. Biol
, vol.13
, pp. 1723-1734
-
-
Han, P.1
Zhang, X.2
Norton, R.S.3
Feng, Z.P.4
-
23
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and Henikoff, J.G. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915-10919.
-
(1992)
Proc. Natl. Acad. Sci
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
24
-
-
34548567232
-
POODLE-L: A two-level SVM prediction system for reliably predicting long disordered regions
-
doi: 10.1093/bioinformatics/btm302
-
Hirose, S., Shimizu, K., Kanai, S., Kuroda, Y., and Noguchi, T. 2007. POODLE-L: A two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics doi: 10.1093/bioinformatics/btm302.
-
(2007)
Bioinformatics
-
-
Hirose, S.1
Shimizu, K.2
Kanai, S.3
Kuroda, Y.4
Noguchi, T.5
-
25
-
-
0000448982
-
Prediction of protein antigenic determinants from amino acid sequences
-
Hopp, T.P. and Woods, K.R. 1981. Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl. Acad. Sci. 78: 3824-3828.
-
(1981)
Proc. Natl. Acad. Sci
, vol.78
, pp. 3824-3828
-
-
Hopp, T.P.1
Woods, K.R.2
-
26
-
-
0020623947
-
A computer program for predicting protein antigenic determinants
-
Hopp, T.P. and Woods, K.R. 1983. A computer program for predicting protein antigenic determinants. Mol. Immunol. 20: 483-489.
-
(1983)
Mol. Immunol
, vol.20
, pp. 483-489
-
-
Hopp, T.P.1
Woods, K.R.2
-
27
-
-
0242362157
-
Prediction of disordered regions in proteins from position specific score matrices
-
Jones, D.T. and Ward, J.J. 2003. Prediction of disordered regions in proteins from position specific score matrices. Proteins (Suppl 6) 53: 573-578.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 573-578
-
-
Jones, D.T.1
Ward, J.J.2
-
28
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14: 1-63.
-
(1959)
Adv. Protein Chem
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
29
-
-
0343621535
-
AAindex: Amino acid index database
-
doi: 10.1093/nar/28.1.374
-
Kawashima, S. and Kanehisa, M. 2000. AAindex: Amino acid index database. Nucleic Acids Res. 28: 374. doi: 10.1093/nar/28.1.374.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 374
-
-
Kawashima, S.1
Kanehisa, M.2
-
30
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J. and Doolittle, R.F. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
-
(1982)
J. Mol. Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
31
-
-
0017157584
-
A simplified representation of protein conformations for rapid simulation of protein folding
-
Levitt, M. 1976. A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104: 59-107.
-
(1976)
J. Mol. Biol
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
32
-
-
0001913048
-
Predicting protein disorder for N-, C-, and internal regions
-
Li, X., Romero, P., Rani, M., Dunker, A.K., and Obradovic, Z. 1999. Predicting protein disorder for N-, C-, and internal regions. Genome Inform. Ser. Workshop Genome Inform. 10: 30-40.
-
(1999)
Genome Inform. Ser. Workshop Genome Inform
, vol.10
, pp. 30-40
-
-
Li, X.1
Romero, P.2
Rani, M.3
Dunker, A.K.4
Obradovic, Z.5
-
33
-
-
0034578463
-
Comparing predictors of disordered protein
-
Li, X., Obradovic, Z., Brown, C.J., Garner, E.C., and Dunker, A.K. 2000. Comparing predictors of disordered protein. Genome Inform. Ser. Workshop Genome Inform. 11: 172-184.
-
(2000)
Genome Inform. Ser. Workshop Genome Inform
, vol.11
, pp. 172-184
-
-
Li, X.1
Obradovic, Z.2
Brown, C.J.3
Garner, E.C.4
Dunker, A.K.5
-
34
-
-
0242458482
-
Protein disorder prediction: Implications for structural proteomics
-
Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J., and Russell, R.B. 2003a. Protein disorder prediction: Implications for structural proteomics. Structure 11: 1453-1459.
-
(2003)
Structure
, vol.11
, pp. 1453-1459
-
-
Linding, R.1
Jensen, L.J.2
Diella, F.3
Bork, P.4
Gibson, T.J.5
Russell, R.B.6
-
35
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
doi: 10.1093/nar/gkg5
-
Linding, R., Russell, R.B., Neduva, V., and Gibson, T.J. 2003b. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res. 31: 3701-3708. doi: 10.1093/nar/gkg5.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
Russell, R.B.2
Neduva, V.3
Gibson, T.J.4
-
36
-
-
10844222539
-
Sequence patterns associated with disordered regions in proteins
-
Lise, S. and Jones, D.T. 2005. Sequence patterns associated with disordered regions in proteins. Proteins 58: 144-150.
-
(2005)
Proteins
, vol.58
, pp. 144-150
-
-
Lise, S.1
Jones, D.T.2
-
37
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., and Teller, E. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21: 1087-1092.
-
(1953)
J. Chem. Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
38
-
-
0022798896
-
Radial locations of amino acid residues in a globular protein: Correlation with the sequence
-
Nishikawa, K. and Ooi, T. 1986. Radial locations of amino acid residues in a globular protein: Correlation with the sequence. J. Biochem. 100: 1043-1047.
-
(1986)
J. Biochem
, vol.100
, pp. 1043-1047
-
-
Nishikawa, K.1
Ooi, T.2
-
39
-
-
0015217634
-
The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale
-
Nozaki, Y. and Tanford, C. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J. Biol. Chem. 246: 2211-2217.
-
(1971)
J. Biol. Chem
, vol.246
, pp. 2211-2217
-
-
Nozaki, Y.1
Tanford, C.2
-
40
-
-
0017689283
-
An analysis of non-bonded energy of proteins
-
Oobatake, M. and Ooi, T. 1977. An analysis of non-bonded energy of proteins. J. Theor. Biol. 67: 567-584.
-
(1977)
J. Theor. Biol
, vol.67
, pp. 567-584
-
-
Oobatake, M.1
Ooi, T.2
-
41
-
-
0034113648
-
β-sheet propensity and its correlation with parameters based on conformation
-
Pal, D. and Chakrabarti, P. 2000. β-sheet propensity and its correlation with parameters based on conformation. Acta Crystallogr. D Biol. Crystallogr. 56: 589-594.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr
, vol.56
, pp. 589-594
-
-
Pal, D.1
Chakrabarti, P.2
-
42
-
-
0020122457
-
Protein secondary structure. Studies on the limits of prediction accuracy
-
Palau, J., Argos, P., and Puigdomenech, P. 1982. Protein secondary structure. Studies on the limits of prediction accuracy. Int. J. Pept. Protein Res. 19: 394-401.
-
(1982)
Int. J. Pept. Protein Res
, vol.19
, pp. 394-401
-
-
Palau, J.1
Argos, P.2
Puigdomenech, P.3
-
43
-
-
33745289067
-
Length-dependent prediction of protein intrinsic disorder
-
doi: 10.1186/1471-2105-7-208
-
Peng, K., Radivojac, P., Vucetic, S., Dunker, A.K., and Obradovic, Z. 2006. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7: 208. doi: 10.1186/1471-2105-7-208.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 208
-
-
Peng, K.1
Radivojac, P.2
Vucetic, S.3
Dunker, A.K.4
Obradovic, Z.5
-
44
-
-
24044515001
-
FoldIndex: A simple tool to predict whether a given protein sequence is intrinsically unfolded
-
Prilusky, J., Felder, C.E., Zeev-Ben-Mordehai, T., Rydberg, E.H., Man, O., Beckmann, J.S., Silman, I., and Sussman, J.L. 2005. FoldIndex: A simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21: 3435-3438.
-
(2005)
Bioinformatics
, vol.21
, pp. 3435-3438
-
-
Prilusky, J.1
Felder, C.E.2
Zeev-Ben-Mordehai, T.3
Rydberg, E.H.4
Man, O.5
Beckmann, J.S.6
Silman, I.7
Sussman, J.L.8
-
45
-
-
0037231039
-
A knowledge-based scale for amino acid membrane propensity
-
Punta, M. and Maritan, A. 2003. A knowledge-based scale for amino acid membrane propensity. Proteins 50: 114-121.
-
(2003)
Proteins
, vol.50
, pp. 114-121
-
-
Punta, M.1
Maritan, A.2
-
46
-
-
33845280446
-
Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
-
Radzicka, A. and Wolfenden, R. 1988. Comparing the polarities of the amino acids: Side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 27: 1664-1670.
-
(1988)
Biochemistry
, vol.27
, pp. 1664-1670
-
-
Radzicka, A.1
Wolfenden, R.2
-
47
-
-
0019443447
-
The anatomy and taxonomy of protein structure
-
Richardson, J.S. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34: 167-339.
-
(1981)
Adv. Protein Chem
, vol.34
, pp. 167-339
-
-
Richardson, J.S.1
-
48
-
-
0030691703
-
Identifying disordered regions in proteins from amino acid sequence
-
Romero, P., Obradovic, Z., Kissinger, C., Villafranca, J.E., and Dunker, A.K. 1997. Identifying disordered regions in proteins from amino acid sequence. Proc. IEEE Int. Conf. Neural Networks 1: 90-95.
-
(1997)
Proc. IEEE Int. Conf. Neural Networks
, vol.1
, pp. 90-95
-
-
Romero, P.1
Obradovic, Z.2
Kissinger, C.3
Villafranca, J.E.4
Dunker, A.K.5
-
49
-
-
0022412192
-
Hydrophobicity of amino acid residues in globular proteins
-
Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H., and Zehfus, M.H. 1985. Hydrophobicity of amino acid residues in globular proteins. Science 229: 834-838.
-
(1985)
Science
, vol.229
, pp. 834-838
-
-
Rose, G.D.1
Geselowitz, A.R.2
Lesser, G.J.3
Lee, R.H.4
Zehfus, M.H.5
-
50
-
-
33750945327
-
A backbone-based theory of protein folding
-
Rose, G.D., Fleming, P.J., Banavar, J.R., and Maritan, A. 2006. A backbone-based theory of protein folding. Proc. Natl. Acad. Sci. 103: 16623-16633.
-
(2006)
Proc. Natl. Acad. Sci
, vol.103
, pp. 16623-16633
-
-
Rose, G.D.1
Fleming, P.J.2
Banavar, J.R.3
Maritan, A.4
-
51
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev, R. and Grishin, N. 2003. COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 326: 317-336.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
52
-
-
34748854289
-
Predicting mostly disordered proteins by using structure-unknown protein data
-
doi: 10.1186/1471-2105-8-78
-
Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., and Noguchi, T. 2007. Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8: 78. doi: 10.1186/1471-2105-8-78.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 78
-
-
Shimizu, K.1
Muraoka, Y.2
Hirose, S.3
Tomii, K.4
Noguchi, T.5
-
53
-
-
33846099868
-
DisProt: The database of disordered proteins
-
doi: 10.1093/nar/gkl
-
Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N., et al. 2007. DisProt: The database of disordered proteins. Nucleic Acids Res. 35: D786-D793. doi: 10.1093/nar/gkl.
-
(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
-
54
-
-
0033529861
-
Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone
-
Street, A.G. and Mayo, S.L. 1999. Intrinsic β-sheet propensities result from van der Waals interactions between side chains and the local backbone. Proc. Natl. Acad. Sci. 96: 9074-9076.
-
(1999)
Proc. Natl. Acad. Sci
, vol.96
, pp. 9074-9076
-
-
Street, A.G.1
Mayo, S.L.2
-
55
-
-
33746952996
-
Protein disorder prediction by condensed PSSM considering propensity for order or disorder
-
doi: 10.1186/1471-2105-7-319
-
Su, C.T., Chen, C.Y., and Ou, Y.Y. 2006. Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics 7: 319. doi: 10.1186/1471-2105-7-319.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 319
-
-
Su, C.T.1
Chen, C.Y.2
Ou, Y.Y.3
-
56
-
-
34250821717
-
Mechanism of coupled folding and binding of an intrinsically disordered protein
-
Sugase, K., Dyson, H.J., and Wright, P.E. 2007. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature 447: 1021-1025.
-
(2007)
Nature
, vol.447
, pp. 1021-1025
-
-
Sugase, K.1
Dyson, H.J.2
Wright, P.E.3
-
57
-
-
0033028454
-
PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations
-
Sunyaev, S.R., Eisenhaber, F., Rodchenkov, I.V., Eisenhaber, B., Tumanyan, V.G., and Kuznetsov, E.N. 1999. PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng. 12: 387-394.
-
(1999)
Protein Eng
, vol.12
, pp. 387-394
-
-
Sunyaev, S.R.1
Eisenhaber, F.2
Rodchenkov, I.V.3
Eisenhaber, B.4
Tumanyan, V.G.5
Kuznetsov, E.N.6
-
58
-
-
0028091659
-
Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
-
Tatusov, R.L., Altschul, S.F., and Koonin, E.V. 1994. Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. 91: 12091-12095.
-
(1994)
Proc. Natl. Acad. Sci
, vol.91
, pp. 12091-12095
-
-
Tatusov, R.L.1
Altschul, S.F.2
Koonin, E.V.3
-
59
-
-
0029922443
-
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
-
Tomii, K. and Kanehisa, M. 1996. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9: 27-36.
-
(1996)
Protein Eng
, vol.9
, pp. 27-36
-
-
Tomii, K.1
Kanehisa, M.2
-
60
-
-
0034669882
-
Why are "natively unfolded" proteins unstructured under physiologic conditions?
-
Uversky, V.N., Gillespie, J.R., and Fink, A.L. 2000. Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41: 415-427.
-
(2000)
Proteins
, vol.41
, pp. 415-427
-
-
Uversky, V.N.1
Gillespie, J.R.2
Fink, A.L.3
-
61
-
-
0028361031
-
Accuracy of protein flexibility predictions
-
Vihinen, M., Torkkila, E., and Riikonen, P. 1994. Accuracy of protein flexibility predictions. Proteins 19: 141-149.
-
(1994)
Proteins
, vol.19
, pp. 141-149
-
-
Vihinen, M.1
Torkkila, E.2
Riikonen, P.3
-
62
-
-
0041418213
-
Flavors of protein disorder
-
Vucetic, S., Brown, C.J., Dunker, A.K., and Obradovic, Z. 2003. Flavors of protein disorder. Proteins 52: 573-584.
-
(2003)
Proteins
, vol.52
, pp. 573-584
-
-
Vucetic, S.1
Brown, C.J.2
Dunker, A.K.3
Obradovic, Z.4
-
63
-
-
33747868721
-
Spritz: A server for the prediction of intrinsically disordered regions in protein sequences using kernel machines
-
doi: 10.1093/nar/gkl166
-
Vullo, A., Bortolami, O., Pollastri, G., and Tosatto, S.C. 2006. Spritz: A server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. Nucleic Acids Res. 34: W164-W168. doi: 10.1093/nar/gkl166.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Vullo, A.1
Bortolami, O.2
Pollastri, G.3
Tosatto, S.C.4
-
64
-
-
34250824619
-
A data-driven, systematic search algorithm for structure determination of denatured or disordered proteins
-
Wang, L. and Donald, B.R. 2006. A data-driven, systematic search algorithm for structure determination of denatured or disordered proteins. Comput. Syst. Bioinformatics Conf. 5: 67-78.
-
(2006)
Comput. Syst. Bioinformatics Conf
, vol.5
, pp. 67-78
-
-
Wang, L.1
Donald, B.R.2
-
65
-
-
1542358787
-
Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
-
Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., and Jones, D.T. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337: 635-645.
-
(2004)
J. Mol. Biol
, vol.337
, pp. 635-645
-
-
Ward, J.J.1
Sodhi, J.S.2
McGuffin, L.J.3
Buxton, B.F.4
Jones, D.T.5
-
66
-
-
0000330322
-
Protein-protein interactions
-
Waugh, D.F. 1954. Protein-protein interactions. Adv. Protein Chem. 9: 325-437.
-
(1954)
Adv. Protein Chem
, vol.9
, pp. 325-437
-
-
Waugh, D.F.1
-
67
-
-
6344277430
-
Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
-
Weathers, E.A., Paulaitis, M.E., Woolf, T.B., and Hoh, J.H. 2004. Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein. FEBS Lett. 576: 348-352.
-
(2004)
FEBS Lett
, vol.576
, pp. 348-352
-
-
Weathers, E.A.1
Paulaitis, M.E.2
Woolf, T.B.3
Hoh, J.H.4
-
68
-
-
0035220932
-
The protein nonfolding problem: Amino acid determinants of intrinsic order and disorder
-
Williams, R.M., Obradovic, Z., Mathura, V., Braun, W., Garner, E.C., Young, J., Takayama, S., Brown, C.J., and Dunker, A.K. 2001. The protein nonfolding problem: Amino acid determinants of intrinsic order and disorder. Pac. Symp. Biocomput. 6: 89-100.
-
(2001)
Pac. Symp. Biocomput
, vol.6
, pp. 89-100
-
-
Williams, R.M.1
Obradovic, Z.2
Mathura, V.3
Braun, W.4
Garner, E.C.5
Young, J.6
Takayama, S.7
Brown, C.J.8
Dunker, A.K.9
-
69
-
-
0030005250
-
Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
-
Wimley, W.C., Creamer, T.P., and White, S.H. 1996. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 35: 5109-5124.
-
(1996)
Biochemistry
, vol.35
, pp. 5109-5124
-
-
Wimley, W.C.1
Creamer, T.P.2
White, S.H.3
-
70
-
-
20744437001
-
RONN: The bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
-
Yang, Z.R., Thomson, R., McNeil, P., and Esnouf, R.M. 2005. RONN: The bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21: 3369-3376.
-
(2005)
Bioinformatics
, vol.21
, pp. 3369-3376
-
-
Yang, Z.R.1
Thomson, R.2
McNeil, P.3
Esnouf, R.M.4
-
71
-
-
0345827721
-
Quantifying the effect of burial of amino acid residues on protein stability
-
Zhou, H. and Zhou, Y. 2004. Quantifying the effect of burial of amino acid residues on protein stability. Proteins 54: 315-322.
-
(2004)
Proteins
, vol.54
, pp. 315-322
-
-
Zhou, H.1
Zhou, Y.2
|