-
1
-
-
0018782641
-
Hierarchic organization of domains in globular proteins
-
Rose G.D. Hierarchic organization of domains in globular proteins. J. Mol. Biol. 134 (1979) 447-470
-
(1979)
J. Mol. Biol.
, vol.134
, pp. 447-470
-
-
Rose, G.D.1
-
2
-
-
0029922493
-
Foldons, protein structural modules, and exons
-
Panchenko A.R., Luthey-Schulten Z., and Wolynes P.G. Foldons, protein structural modules, and exons. Proc. Natl Acad. Sci. USA 93 (1996) 2008-2013
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 2008-2013
-
-
Panchenko, A.R.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
4
-
-
0344527798
-
Structural analyses of CREB-CBP transcriptional activator-coactivator complexes by NMR spectroscopy: implications for mapping the boundaries of structural domains
-
Radhakrishnan I., Perez-Alvarado G.C., Parker D., Dyson H.J., Montminy M.R., and Wright P.E. Structural analyses of CREB-CBP transcriptional activator-coactivator complexes by NMR spectroscopy: implications for mapping the boundaries of structural domains. J. Mol. Biol. 287 (1999) 859-865
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 859-865
-
-
Radhakrishnan, I.1
Perez-Alvarado, G.C.2
Parker, D.3
Dyson, H.J.4
Montminy, M.R.5
Wright, P.E.6
-
6
-
-
33746338567
-
Partitioning protein structures into domains: why is it so difficult?
-
Holland T.A., Veretnik S., Shindyalov I.N., and Bourne P.E. Partitioning protein structures into domains: why is it so difficult?. J. Mol. Biol. 361 (2006) 562-590
-
(2006)
J. Mol. Biol.
, vol.361
, pp. 562-590
-
-
Holland, T.A.1
Veretnik, S.2
Shindyalov, I.N.3
Bourne, P.E.4
-
8
-
-
0037460953
-
DomCut: prediction of inter-domain linker regions in amino acid sequences
-
Suyama M., and Ohara O. DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics 19 (2003) 673-674
-
(2003)
Bioinformatics
, vol.19
, pp. 673-674
-
-
Suyama, M.1
Ohara, O.2
-
9
-
-
0036893072
-
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
-
Marsden R.L., McGuffin L.J., and Jones D.T. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci. 11 (2002) 2814-2824
-
(2002)
Protein Sci.
, vol.11
, pp. 2814-2824
-
-
Marsden, R.L.1
McGuffin, L.J.2
Jones, D.T.3
-
10
-
-
32144434539
-
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
-
Gewehr J.E., and Zimmer R. SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 22 (2006) 181-187
-
(2006)
Bioinformatics
, vol.22
, pp. 181-187
-
-
Gewehr, J.E.1
Zimmer, R.2
-
11
-
-
33947385412
-
Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index
-
Sikder A.R., and Zomaya A.Y. Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index. BMC Bioinformatics 7 Suppl 5 (2006) S6
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 5
-
-
Sikder, A.R.1
Zomaya, A.Y.2
-
12
-
-
0036288851
-
Characterization and prediction of linker sequences of multi-domain proteins by a neural network
-
Miyazaki S., Kuroda Y., and Yokoyama S. Characterization and prediction of linker sequences of multi-domain proteins by a neural network. J. Struct. Funct. Genomics 2 (2002) 37-51
-
(2002)
J. Struct. Funct. Genomics
, vol.2
, pp. 37-51
-
-
Miyazaki, S.1
Kuroda, Y.2
Yokoyama, S.3
-
14
-
-
3042810008
-
Sequence-based prediction of protein domains
-
Liu J., and Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res. 32 (2004) 3522-3530
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3522-3530
-
-
Liu, J.1
Rost, B.2
-
15
-
-
17844363963
-
PPRODO: prediction of protein domain boundaries using neural networks
-
Sim J., Kim S.Y., and Lee J. PPRODO: prediction of protein domain boundaries using neural networks. Proteins 59 (2005) 627-632
-
(2005)
Proteins
, vol.59
, pp. 627-632
-
-
Sim, J.1
Kim, S.Y.2
Lee, J.3
-
16
-
-
45249093424
-
DomNet: protein domain boundary prediction using enhanced general regression network and new profiles
-
Yoo P.D., Sikder A.R., Taheri J., Zhou B.B., and Zomaya A.Y. DomNet: protein domain boundary prediction using enhanced general regression network and new profiles. IEEE Trans. Nanobiosci. 7 (2008) 172-181
-
(2008)
IEEE Trans. Nanobiosci.
, vol.7
, pp. 172-181
-
-
Yoo, P.D.1
Sikder, A.R.2
Taheri, J.3
Zhou, B.B.4
Zomaya, A.Y.5
-
17
-
-
33747836566
-
KemaDom: a Web server for domain prediction using kernel machine with local context
-
Chen L., Wang W., Ling S., Jia C., and Wang F. KemaDom: a Web server for domain prediction using kernel machine with local context. Nucleic Acids Res. 34 (2006) W158-W163
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Chen, L.1
Wang, W.2
Ling, S.3
Jia, C.4
Wang, F.5
-
18
-
-
3142680264
-
Automatic prediction of protein domains from sequence information using a hybrid learning system
-
Nagarajan N., and Yona G. Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics 20 (2004) 1335-1360
-
(2004)
Bioinformatics
, vol.20
, pp. 1335-1360
-
-
Nagarajan, N.1
Yona, G.2
-
19
-
-
33745101459
-
DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
-
Cheng J., Sweredoski M.J., and Baldi P. DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Min. Knowl. Discov. 13 (2006) 1-10
-
(2006)
Data Min. Knowl. Discov.
, vol.13
, pp. 1-10
-
-
Cheng, J.1
Sweredoski, M.J.2
Baldi, P.3
-
20
-
-
21744461895
-
Armadillo: domain boundary prediction by amino acid composition
-
Dumontier M., Yao R., Feldman H.J., and Hogue C.W. Armadillo: domain boundary prediction by amino acid composition. J. Mol. Biol. 350 (2005) 1061-1073
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 1061-1073
-
-
Dumontier, M.1
Yao, R.2
Feldman, H.J.3
Hogue, C.W.4
-
21
-
-
34247560816
-
Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone
-
Dovidchenko N.V., Yu Lobanov M., and Galzitskaya O.V. Prediction of number and position of domain boundaries in multi-domain proteins by use of amino acid sequence alone. Curr. Protein Pept. Sci. 8 (2007) 189-195
-
(2007)
Curr. Protein Pept. Sci.
, vol.8
, pp. 189-195
-
-
Dovidchenko, N.V.1
Yu Lobanov, M.2
Galzitskaya, O.V.3
-
22
-
-
0036306348
-
SnapDRAGON: a method to delineate protein structural domains from sequence data
-
George R.A., and Heringa J. SnapDRAGON: a method to delineate protein structural domains from sequence data. J. Mol. Biol. 316 (2002) 839-851
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 839-851
-
-
George, R.A.1
Heringa, J.2
-
23
-
-
30344438515
-
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM
-
Kim D.E., Chivian D., Malmstrom L., and Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins 61 Suppl 7 (2005) 193-200
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 193-200
-
-
Kim, D.E.1
Chivian, D.2
Malmstrom, L.3
Baker, D.4
-
24
-
-
0029097099
-
Global fold determination from a small number of distance restraints
-
Aszodi A., Gradwell M.J., and Taylor W.R. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251 (1995) 308-326
-
(1995)
J. Mol. Biol.
, vol.251
, pp. 308-326
-
-
Aszodi, A.1
Gradwell, M.J.2
Taylor, W.R.3
-
25
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., and Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34 (1999) 82-95
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
26
-
-
34547591340
-
DOMAC: an accurate, hybrid protein domain prediction server
-
Cheng J. DOMAC: an accurate, hybrid protein domain prediction server. Nucleic Acids Res. 35 (2007) W354-W356
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Cheng, J.1
-
27
-
-
20844435796
-
Meta-DP: domain prediction meta-server
-
Saini H.K., and Fischer D. Meta-DP: domain prediction meta-server. Bioinformatics 21 (2005) 2917-2920
-
(2005)
Bioinformatics
, vol.21
, pp. 2917-2920
-
-
Saini, H.K.1
Fischer, D.2
-
28
-
-
34247566179
-
Computer-assisted protein domain boundary prediction using the Dom-Pred server
-
Bryson K., Cozzetto D., and Jones D.T. Computer-assisted protein domain boundary prediction using the Dom-Pred server. Curr. Protein Pept. Sci. 8 (2007) 181-188
-
(2007)
Curr. Protein Pept. Sci.
, vol.8
, pp. 181-188
-
-
Bryson, K.1
Cozzetto, D.2
Jones, D.T.3
-
29
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
30
-
-
58149342116
-
-
Guoguang, L. (1999). DOMID. Version 1.0 Mar-15-1999. Karolinska Institute. Version 2.5 Nov-9-1999 Lund Univ.
-
Guoguang, L. (1999). DOMID. Version 1.0 Mar-15-1999. Karolinska Institute. Version 2.5 Nov-9-1999 Lund Univ.
-
-
-
-
31
-
-
0032951163
-
Protein structural domain identification
-
Taylor W.R. Protein structural domain identification. Protein Eng. 12 (1999) 203-216
-
(1999)
Protein Eng.
, vol.12
, pp. 203-216
-
-
Taylor, W.R.1
-
32
-
-
0037252685
-
MMDB: Entrez's 3D-structure database
-
Chen J., Anderson J.B., DeWeese-Scott C., Fedorova N.D., Geer L.Y., He S., et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31 (2003) 474-477
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 474-477
-
-
Chen, J.1
Anderson, J.B.2
DeWeese-Scott, C.3
Fedorova, N.D.4
Geer, L.Y.5
He, S.6
-
33
-
-
30344468122
-
Domain definition and target classification for CASP6
-
Tress M., Tai C.H., Wang G., Ezkurdia I., Lopez G., Valencia A., Lee B., and Dunbrack Jr. R.L. Domain definition and target classification for CASP6. Proteins 61 Suppl 7 (2005) 8-18
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 8-18
-
-
Tress, M.1
Tai, C.H.2
Wang, G.3
Ezkurdia, I.4
Lopez, G.5
Valencia, A.6
Lee, B.7
Dunbrack Jr., R.L.8
-
34
-
-
0037377548
-
Prediction of protein domain boundaries from sequence alone
-
Galzitskaya O.V., and Melnik B.S. Prediction of protein domain boundaries from sequence alone. Protein Sci. 12 (2003) 696-701
-
(2003)
Protein Sci.
, vol.12
, pp. 696-701
-
-
Galzitskaya, O.V.1
Melnik, B.S.2
-
35
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
36
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
-
(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
-
37
-
-
23144463912
-
FFAS03: a server for profile-profile sequence alignments
-
Jaroszewski L., Rychlewski L., Li Z., Li W., and Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33 (2005) W284-W288
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Jaroszewski, L.1
Rychlewski, L.2
Li, Z.3
Li, W.4
Godzik, A.5
-
38
-
-
0033011876
-
Protein structure comparison using iterated double dynamic programming
-
Taylor W.R. Protein structure comparison using iterated double dynamic programming. Protein Sci. 8 (1999) 654-665
-
(1999)
Protein Sci.
, vol.8
, pp. 654-665
-
-
Taylor, W.R.1
-
39
-
-
36749014942
-
Assessment of predictions submitted for the CASP7 domain prediction category
-
Tress M., Cheng J., Baldi P., Joo K., Lee J., Seo J.H., et al. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins 69 Suppl 8 (2007) 137-151
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 137-151
-
-
Tress, M.1
Cheng, J.2
Baldi, P.3
Joo, K.4
Lee, J.5
Seo, J.H.6
-
42
-
-
0034491038
-
Protein domain decomposition using a graph-theoretic approach
-
Xu Y., Xu D., and Gabow H.N. Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16 (2000) 1091-1104
-
(2000)
Bioinformatics
, vol.16
, pp. 1091-1104
-
-
Xu, Y.1
Xu, D.2
Gabow, H.N.3
-
43
-
-
0028838717
-
Threading a database of protein cores
-
Madej T., Gibrat J.F., and Bryant S.H. Threading a database of protein cores. Proteins 23 (1995) 356-369
-
(1995)
Proteins
, vol.23
, pp. 356-369
-
-
Madej, T.1
Gibrat, J.F.2
Bryant, S.H.3
-
45
-
-
0028290005
-
Parser for protein folding units
-
Holm L., and Sander C. Parser for protein folding units. Proteins 19 (1994) 256-268
-
(1994)
Proteins
, vol.19
, pp. 256-268
-
-
Holm, L.1
Sander, C.2
-
46
-
-
20444490870
-
Determining protein topology from skeletons of secondary structures
-
Wu Y., Chen M., Lu M., Wang Q., and Ma J. Determining protein topology from skeletons of secondary structures. J. Mol. Biol. 350 (2005) 571-586
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 571-586
-
-
Wu, Y.1
Chen, M.2
Lu, M.3
Wang, Q.4
Ma, J.5
-
47
-
-
0043180474
-
PISCES: a protein sequence culling server
-
Wang G., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
-
(2003)
Bioinformatics
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
48
-
-
0002087305
-
Hard convex body fluids
-
Prigogine I., and Rice S.A. (Eds), John Wiley Sons, Inc., New York, NY
-
Allen M.P., Evans G.T., Frenkel D., and Mulder B.M. Hard convex body fluids. In: Prigogine I., and Rice S.A. (Eds). Advances in Chemical Physics 86 (2007), John Wiley Sons, Inc., New York, NY 1-166
-
(2007)
Advances in Chemical Physics
, vol.86
, pp. 1-166
-
-
Allen, M.P.1
Evans, G.T.2
Frenkel, D.3
Mulder, B.M.4
-
49
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar I., and Jernigan R.L. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266 (1997) 195-214
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
50
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
|