-
1
-
-
0033954256
-
The protein data bank
-
Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
2
-
-
0345600222
-
MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification
-
Bindewald,E. et al. (2003) MANIFOLD: Protein fold recognition based on secondary structure, sequence similarity and enzyme classification. Protein Eng., 16, 785-789.
-
(2003)
Protein Eng.
, vol.16
, pp. 785-789
-
-
Bindewald, E.1
-
3
-
-
0348129526
-
The ASTRAL compendium in 2004
-
Chandonia,J.M. et al. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, D189-D192.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Chandonia, J.M.1
-
4
-
-
33749570293
-
DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neutral networks
-
in press
-
Cheng,J. et al. (2005) DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neutral networks. Data Mining Knowl. Discov. in press, (http://www.ics.uci.edu/~baldig/dompro.html).
-
(2005)
Data Mining Knowl. Discov.
-
-
Cheng, J.1
-
5
-
-
10744230917
-
Automated prediction of CASP-5 structures using the Robetta server
-
Chivian,D. et al. (2003) Automated prediction of CASP-5 structures using the Robetta server. Proteins, 53, 524-533.
-
(2003)
Proteins
, vol.53
, pp. 524-533
-
-
Chivian, D.1
-
6
-
-
2942576060
-
Enhanced protein domain discovery using taxonomy
-
Coin,L. et al. (2004) Enhanced protein domain discovery using taxonomy. BMC Bioinfomatics, 5, 56.
-
(2004)
BMC Bioinfomatics
, vol.5
, pp. 56
-
-
Coin, L.1
-
7
-
-
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, 1061-73.
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 1061-1073
-
-
Dumontier, M.1
-
8
-
-
0242299155
-
CAFASP3: The third critical assessment of fully automated structure prediciton methods
-
Fischer,D. et al. (2003) CAFASP3: The third critical assessment of fully automated structure prediciton methods. Proteins, 53, 503-516.
-
(2003)
Proteins
, vol.53
, pp. 503-516
-
-
Fischer, D.1
-
9
-
-
13844292778
-
The SSEA server for protein secondary structure alignment
-
Fontana,P. et al. (2005) The SSEA server for protein secondary structure alignment. Bioinformatics, 21, 393-395.
-
(2005)
Bioinformatics
, vol.21
, pp. 393-395
-
-
Fontana, P.1
-
10
-
-
0036721254
-
Protein domain identification and improved sequence similarity searching using PSI-BLAST
-
George,R.A. and Heringa,J. (2002a) Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins, 48, 672-681.
-
(2002)
Proteins
, vol.48
, pp. 672-681
-
-
George, R.A.1
Heringa, J.2
-
11
-
-
0036306348
-
SnapDRAGON: A method to delineate protein structural domains from sequence data
-
George,R.A. and Heringa,J. (2002b) 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
-
12
-
-
0033563522
-
Whole genome protein domain analysis using a new method for domain clustering
-
Gouzy,J. et al. (1999) Whole genome protein domain analysis using a new method for domain clustering. Comp. Chem., 23, 333-340.
-
(1999)
Comp. Chem.
, vol.23
, pp. 333-340
-
-
Gouzy, J.1
-
13
-
-
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
-
14
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
15
-
-
0031889752
-
Domain assignment for protein structures using a consensus approach: Characterisation and analysis
-
Jones,S. et al. (1998) Domain assignment for protein structures using a consensus approach: Characterisation and analysis. Protein Sci., 7, 233-242.
-
(1998)
Protein Sci.
, vol.7
, pp. 233-242
-
-
Jones, S.1
-
16
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch,W. and Sander,C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
17
-
-
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
-
18
-
-
0042622240
-
GlobPlot: Exploring protein sequences for globularity and disorder
-
Linding,R. et al. (2003) GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res., 31, 3701-3708.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3701-3708
-
-
Linding, R.1
-
19
-
-
0037305939
-
Domains, motifs and clusters in the protein universe
-
Liu,J. and Rost,B. (2003) Domains, motifs and clusters in the protein universe. Curr. Opin. Chem. Biol., 7, 5-11.
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 5-11
-
-
Liu, J.1
Rost, B.2
-
20
-
-
0036893072
-
Rapid protein domain assignment from amino acid sequence using predicted secondary structure
-
Marsden,R.L. et al. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci., 11, 2814-2824.
-
(2002)
Protein Sci.
, vol.11
, pp. 2814-2824
-
-
Marsden, R.L.1
-
21
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
McGuffin,L.J. and Jones,D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
22
-
-
0035109761
-
What are the baselines for protein fold recognition?
-
McGuffin,L.J. et al. (2001) What are the baselines for protein fold recognition?. Bioinformatics, 17, 63-72.
-
(2001)
Bioinformatics
, vol.17
, pp. 63-72
-
-
McGuffin, L.J.1
-
23
-
-
30344459116
-
Critical assessment of methods of protein structure prediction (CASP)-round VI
-
Moult,J. et al. (2005) Critical assessment of methods of protein structure prediction (CASP)-round VI. Proteins, 61, Suppl 7, 3-7.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 3-7
-
-
Moult, J.1
-
24
-
-
0037251964
-
The InterPro database, 2003 brings increased coverage and new features
-
Mulder,N.J. et al. (2003) The InterPro database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 315-318
-
-
Mulder, N.J.1
-
25
-
-
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
-
26
-
-
3142680264
-
Automatic prediction of protein domains from sequence information using a hybrid learning system
-
Nagarajan,N. and Yona,G. (2004) Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics, 20, 1335-1360.
-
(2004)
Bioinformatics
, vol.20
, pp. 1335-1360
-
-
Nagarajan, N.1
Yona, G.2
-
27
-
-
0031874788
-
DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
-
Park,J. and Teichmann,S.A. (1998) DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics, 14, 144-150.
-
(1998)
Bioinformatics
, vol.14
, pp. 144-150
-
-
Park, J.1
Teichmann, S.A.2
-
28
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
Rychlewski,L. et al. (2000) Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci., 9, 232-241.
-
(2000)
Protein Sci.
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
-
29
-
-
20844435796
-
Meta-DP: Domain prediction meta-server
-
Saini,H.K. and Fischer,D. (2005) Meta-DP: Domain prediction meta-server. Bioinformatics, 21, 2917-2920.
-
(2005)
Bioinformatics
, vol.21
, pp. 2917-2920
-
-
Saini, H.K.1
Fischer, D.2
-
30
-
-
0043123160
-
SSEP: Secondary structural elements of proteins
-
Shanthi,V. et al. (2003) SSEP: Secondary structural elements of proteins. Nucleic Acids Res., 31, 3404-3405.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3404-3405
-
-
Shanthi, V.1
-
31
-
-
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
-
32
-
-
30344442775
-
Evaluation of domain prediction in CASP6
-
Tai,C.H. et al. (2005) Evaluation of domain prediction in CASP6. Proteins, 61, Suppl 7, 183-92.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 183-1892
-
-
Tai, C.H.1
-
33
-
-
12344261833
-
The relationship between domain duplication and recombination
-
Vogel,C. et al. (2005) The relationship between domain duplication and recombination. J. Mol. Biol., 346, 355-365.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 355-365
-
-
Vogel, C.1
-
34
-
-
84959053798
-
Improving profile-profile alignment via log average scoring
-
Gascuel,O. and Moret,B.M.E (eds). Aarhus, Denmark, August 2001, LNCS Springer-Verlag, Berlin, Heidelberg, NY
-
von Öhsen,N. and Zimmer.R. (2001) Improving profile-profile alignment via log average scoring. In Gascuel,O. and Moret,B.M.E (eds). In Proceedings of the First International Workshop, WABI 2001, Algorithms in Bioinformatics, Aarhus, Denmark, August 2001, LNCS 2149, pp. 11-26. Springer-Verlag, Berlin, Heidelberg, NY.
-
(2001)
Proceedings of the First International Workshop WABI 2001, Algorithms in Bioinformatics
, vol.2149
, pp. 11-26
-
-
von Öhsen, N.1
Zimmer, R.2
-
35
-
-
0043130635
-
Profile-profile alignment: A powerful tool for protein structure prediction
-
Altman,R.B., Dunker,A.K., Hunter,L., Jung,T.A and Klein,T.E. (eds). World Scientific Publishing Co. Pte. Ltd., Singapore
-
von Öhsen,N., Sommer,I. and Zimmer,R. (2003) Profile-profile alignment: A powerful tool for protein structure prediction. In Altman,R.B., Dunker,A.K., Hunter,L., Jung,T.A and Klein,T.E. (eds). Pacific Symposium on Biocomputing 2003, World Scientific Publishing Co. Pte. Ltd., Singapore, pp. 252-263.
-
(2003)
Pacific Symposium on Biocomputing 2003
, pp. 252-263
-
-
von Öhsen, N.1
Sommer, I.2
Zimmer, R.3
-
36
-
-
4143083332
-
Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
-
von Öhsen,N. et al. (2004) Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics, 20, 2228-2235.
-
(2004)
Bioinformatics
, vol.20
, pp. 2228-2235
-
-
von Öhsen, N.1
-
37
-
-
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
-
38
-
-
0036307493
-
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
-
Yona,G. and Levitt,M. (2002) Within the twilight zone: A sensitive profile-profile comparison tool based on information theory. J. Mol. Biol., 315, 1257-1275.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
|