-
1
-
-
59649123454
-
FIEFDom: A transparent domain boundary recognition system using a fuzzy mean operator
-
Bondugula, R. et al. (2009) FIEFDom: A transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Res., 37, 452-462.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 452-462
-
-
Bondugula, R.1
-
2
-
-
33745101459
-
DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks
-
Cheng, J. et al. (2006) DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Min. Knowl. Discov., 13, 1-10.
-
(2006)
Data Min. Knowl. Discov.
, vol.13
, pp. 1-10
-
-
Cheng, J.1
-
3
-
-
78149462514
-
Detailed analysis of function divergence in a large and diverse domain superfamily: Toward a refined protocol of function classification
-
Dessailly, B.H. et al. (2010) Detailed analysis of function divergence in a large and diverse domain superfamily: Toward a refined protocol of function classification. Structure, 18, 1522-1535.
-
(2010)
Structure
, vol.18
, pp. 1522-1535
-
-
Dessailly, B.H.1
-
4
-
-
21744461895
-
Armadillo: Domain boundary prediction by amino acid composition
-
Dumontier, M. et al. (2005) Armadillo: Domain boundary prediction by amino acid composition. J. Mol. Biol., 350, 1061-1073.
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 1061-1073
-
-
Dumontier, M.1
-
5
-
-
79951527638
-
DROP: An SVMdomain linker predictor trained with optimal features selected by
-
random forest
-
Ebina, T. et al. (2011) DROP: An SVMdomain linker predictor trained with optimal features selected by random forest. Bioinformatics, 27, 487-494.
-
(2011)
Bioinformatics
, vol.27
, pp. 487-494
-
-
Ebina, T.1
-
6
-
-
79351469227
-
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning
-
Eickholt, J. et al. (2011) DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. BMC Bioinformatics, 12, 43.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 43
-
-
Eickholt, J.1
-
7
-
-
74249108517
-
Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
-
Ezkurdia, I. et al. (2009) Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins, 77 (Suppl. 9), 196-209.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL.9
, pp. 196-209
-
-
Ezkurdia, I.1
-
8
-
-
75549090603
-
The Pfam protein families database
-
Finn, R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res, 38, D211-D222.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Finn, R.D.1
-
9
-
-
0036306348
-
SnapDRAGON: A method to delineate protein structural domains from sequence data
-
George, R.A. and Heringa, J. (2002) SnapDRAGON: A method to delineate protein structural domains from sequence data. J. Mol. Biol., 316, 839-851.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 839-851
-
-
George, R.A.1
Heringa, J.2
-
10
-
-
0037414465
-
Exhaustive enumeration of protein domain families
-
Heger, A. and Holm, L. (2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749-767.
-
(2003)
J. Mol. Biol.
, vol.328
, pp. 749-767
-
-
Heger, A.1
Holm, L.2
-
11
-
-
13444250007
-
ADDA: A domain database with global coverage of the protein universe
-
Heger, A. et al. (2005) ADDA: A domain database with global coverage of the protein universe. Nucleic Acids Res., 33, D188-D191.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Heger, A.1
-
12
-
-
0032438987
-
HiddenMarkov models for detecting remote protein homologies
-
Karplus, K. et al. (1998) HiddenMarkov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
-
13
-
-
30344438515
-
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM
-
Kim, D.E. et al. (2005) Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins, 61 (Suppl. 7), 193-200.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL.7
, pp. 193-200
-
-
Kim, D.E.1
-
14
-
-
2442499624
-
CHOP proteins into structural domain-like fragments
-
Liu, J. and Rost, B. (2004) CHOP proteins into structural domain-like fragments. Proteins, 55, 678-688.
-
(2004)
Proteins
, vol.55
, pp. 678-688
-
-
Liu, J.1
Rost, B.2
-
15
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
-
16
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo, C.A. et al. (1997) CATH - A hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
-
17
-
-
33746962182
-
Everest: Automatic identification and classification of protein domains in all protein sequences
-
Portugaly, E. et al. (2006) EVEREST: Automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics, 7, 277.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 277
-
-
Portugaly, E.1
-
18
-
-
33745727120
-
Structural diversity of domain superfamilies in the CATH database
-
Reeves, G.A. et al. (2006) Structural diversity of domain superfamilies in the CATH database. J. Mol. Biol., 360, 725-741.
-
(2006)
J. Mol. Biol.
, vol.360
, pp. 725-741
-
-
Reeves, G.A.1
-
19
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
20
-
-
0000120520
-
ProDom: Automated clustering of homologous domains
-
Servant, F. et al. (2002) ProDom: Automated clustering of homologous domains. Brief. Bioinform., 3, 246-251.
-
(2002)
Brief. Bioinform.
, vol.3
, pp. 246-251
-
-
Servant, F.1
-
21
-
-
17844363963
-
Pprodo: Prediction of protein domain boundaries using neural networks
-
Sim, J. et al. (2005) PPRODO: Prediction of protein domain boundaries using neural networks. Proteins, 59, 627-632.
-
(2005)
Proteins
, vol.59
, pp. 627-632
-
-
Sim, J.1
-
22
-
-
0037460953
-
DomCut: Prediction of inter-domain linker regions in amino acid sequences
-
Suyama, M. and Ohara, O. (2003) DomCut: Prediction of inter-domain linker regions in amino acid sequences. Bioinformatics, 19, 673-674.
-
(2003)
Bioinformatics
, vol.19
, pp. 673-674
-
-
Suyama, M.1
Ohara, O.2
-
23
-
-
84855290452
-
Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures
-
Szilagyi, A. et al. (2012) Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures. J. Mol. Biol., 415, 221-235.
-
(2012)
J. Mol. Biol.
, vol.415
, pp. 221-235
-
-
Szilagyi, A.1
-
24
-
-
30344442775
-
Evaluation of domain prediction in CASP6
-
Tai, C.H. et al. (2005) Evaluation of domain prediction in CASP6. Proteins, 61 (Suppl. 7), 183-192.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL.7
, pp. 183-192
-
-
Tai, C.H.1
-
25
-
-
36749014942
-
Assessment of predictions submitted for the CASP7 domain prediction category
-
Tress, M. et al. (2007) Assessment of predictions submitted for the CASP7 domain prediction category. Proteins, 69 (Suppl. 8), 137-151.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL.8
, pp. 137-151
-
-
Tress, M.1
-
26
-
-
0043180474
-
Pisces: A protein sequence culling server
-
Wang, G. and Dunbrack, R.L. (2003) PISCES: A protein sequence culling server. Biopolymers, 19, 1589-1591.
-
(2003)
Biopolymers
, vol.19
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.2
-
27
-
-
0033753811
-
Domain size distributions can predict domain boundaries
-
Wheelan, S.J. et al. (2000) Domain size distributions can predict domain boundaries. Bioinformatics, 16, 613-618.
-
(2000)
Bioinformatics
, vol.16
, pp. 613-618
-
-
Wheelan, S.J.1
-
28
-
-
34249869832
-
Ab initio modeling of small proteins by iterative tasser simulations
-
Wu, S. et al. (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol., 5, 17.
-
(2007)
BMC Biol.
, vol.5
, pp. 17
-
-
Wu, S.1
-
29
-
-
46449123146
-
Muster: Improving protein sequence profile-profile alignments by using multiple sources of structure information
-
Wu, S. and Zhang, Y. (2008) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins, 72, 547-556.
-
(2008)
Proteins
, vol.72
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
30
-
-
34250851687
-
Lomets: A local meta-threading-server for protein structure prediction
-
Wu, S.T. and Zhang, Y. (2007) LOMETS: A local meta-threading-server for protein structure prediction. Nucleic Acids. Res., 35, 3375-3382.
-
(2007)
Nucleic Acids. Res.
, vol.35
, pp. 3375-3382
-
-
Wu, S.T.1
Zhang, Y.2
-
31
-
-
58149336791
-
OPUS-Dom: Applying the folding-based method VECFOLD to determine protein domain boundaries
-
Wu, Y. et al. (2009) OPUS-Dom: Applying the folding-based method VECFOLD to determine protein domain boundaries. J. Mol. Biol., 385, 1314-1329.
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 1314-1329
-
-
Wu, Y.1
-
32
-
-
0034663738
-
Protein threading using prospect: Design and evaluation
-
Xu, Y. and Xu, D. (2000) Protein threading using PROSPECT: Design and evaluation. Proteins, 40, 343-354.
-
(2000)
Proteins
, vol.40
, pp. 343-354
-
-
Xu, Y.1
Xu, D.2
-
33
-
-
0034491038
-
Protein domain decomposition using a graph-theoretic approach
-
Xu, Y. et al. (2000) Protein domain decomposition using a graph-theoretic approach. Bioinformatics, 16, 1091-1104.
-
(2000)
Bioinformatics
, vol.16
, pp. 1091-1104
-
-
Xu, Y.1
-
34
-
-
45249093424
-
DomNet: Protein domain boundary prediction using enhanced general regression network and new profiles
-
Yoo, P.D. et al. (2008) DomNet: Protein domain boundary prediction using enhanced general regression network and new profiles. IEEE Trans. Nanobiosci., 7, 172-181.
-
(2008)
IEEE Trans. Nanobiosci.
, vol.7
, pp. 172-181
-
-
Yoo, P.D.1
-
35
-
-
36749061828
-
Template-based modeling and free modeling by I-TASSER in CASP7
-
Zhang, Y. (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins, 69, 108-117.
-
(2007)
Proteins
, vol.69
, pp. 108-117
-
-
Zhang, Y.1
-
36
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Zhang, Y. (2008) Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol., 18, 342-348.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 342-348
-
-
Zhang, Y.1
-
37
-
-
74249106219
-
I-Tasser: Fully automated protein structure prediction in CASP8
-
Zhang, Y. (2009) I-TASSER: Fully automated protein structure prediction in CASP8. Proteins, 77, 100-113.
-
(2009)
Proteins
, vol.77
, pp. 100-113
-
-
Zhang, Y.1
-
38
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou, H. and Zhou, Y. (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins, 58, 321-328.
-
(2005)
Proteins
, vol.58
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
|