-
1
-
-
0028289467
-
Issues in searching molecular sequence databases
-
Altschul SF, Boguski MS, Gish W, Wootton JC: Issues in searching molecular sequence databases. Nature Genet 1994, 6:119-129.
-
(1994)
Nature Genet.
, vol.6
, pp. 119-129
-
-
Altschul, S.F.1
Boguski, M.S.2
Gish, W.3
Wootton, J.C.4
-
2
-
-
0024328791
-
A holistic approach to protein structure alignment
-
Taylor WR, Orengo CA: A holistic approach to protein structure alignment. Protein Eng 1989, 2:505-519.
-
(1989)
Protein Eng.
, vol.2
, pp. 505-519
-
-
Taylor, W.R.1
Orengo, C.A.2
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
3242876311
-
BLAST: At the core of a powerful and diverse set of sequence analysis tools
-
McGinnis S, Madden TL: BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004, 32:W20-W25.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
McGinnis, S.1
Madden, T.L.2
-
6
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson W, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85(8):2444-2448.
-
(1988)
Proc. Natl. Acad. Sci. U. S. A.
, vol.85
, Issue.8
, pp. 2444-2448
-
-
Pearson, W.1
Lipman, D.J.2
-
7
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson WR: Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 1991, 11(3):635-650.
-
(1991)
Genomics
, vol.11
, Issue.3
, pp. 635-650
-
-
Pearson, W.R.1
-
8
-
-
0019887799
-
Identification of Common Molecular Subsequences
-
Smith TF, Waterman MS: Identification of Common Molecular Subsequences. J Mol Bio 1981, 147:195-197.
-
(1981)
J. Mol. Bio.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
9
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
10
-
-
0036304230
-
Protein fold similarity estimated by a probabilistic approach based on C([alpha])-C([alpha]) distance comparison
-
Carugo O, Pongor S: Protein fold similarity estimated by a probabilistic approach based on C([alpha])-C([alpha]) distance comparison. J Mol Biol 2002, 315:887-898.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 887-898
-
-
Carugo, O.1
Pongor, S.2
-
11
-
-
0029884395
-
A general method for fast multiple sequence alignment
-
Tonges U, Perrey SW, Stoye J, Dress AW: A general method for fast multiple sequence alignment. Gene 1996, 172:GC33-41.
-
(1996)
Gene
, vol.172
-
-
Tonges, U.1
Perrey, S.W.2
Stoye, J.3
Dress, A.W.4
-
12
-
-
0033631725
-
Multiple protein sequence alignment using double-dynamic programming
-
Taylor WR, Saelensminde G, Eidhammer I: Multiple protein sequence alignment using double-dynamic programming. Comput Chem 2000, 24:3-12.
-
(2000)
Comput. Chem.
, vol.24
, pp. 3-12
-
-
Taylor, W.R.1
Saelensminde, G.2
Eidhammer, I.3
-
13
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
14
-
-
13244299130
-
Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
-
Neuwald AF, Liu JS: Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model. BMC Bioinformatics 2004, 5:157.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 157
-
-
Neuwald, A.F.1
Liu, J.S.2
-
16
-
-
0027968068
-
Clustal W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ: Clustal W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
17
-
-
0012293533
-
Homology Induction: The use of machine learning to improve sequence similarity searches
-
Karwath A, King RD: Homology Induction: the use of machine learning to improve sequence similarity searches. BMC Bioinformatics 2002, 3:11.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 11
-
-
Karwath, A.1
King, R.D.2
-
18
-
-
0029006770
-
Comparison of methods for searching protein sequence databases
-
Pearson WR: Comparison of methods for searching protein sequence databases. Protein Sci 1995, 4:1145-1160.
-
(1995)
Protein Sci.
, vol.4
, pp. 1145-1160
-
-
Pearson, W.R.1
-
19
-
-
17344389389
-
Sensitivity and selectivity in protein similarity searches: A comparison of Smith-Waterman in hardware to BLAST and FASTA
-
T H
-
Shpaer EG, Robinson M, Yee D, Candlin JD, Mines RTH, T H: Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA. Genomics 1996, 38(2):179-191.
-
(1996)
Genomics
, vol.38
, Issue.2
, pp. 179-191
-
-
Shpaer, E.G.1
Robinson, M.2
Yee, D.3
Candlin, J.D.4
Mines, R.T.H.5
-
20
-
-
0031760323
-
A Web server to locate periodicities in a sequence
-
J HS
-
Pasquier CM, Promponas VI, Varvayannis NJ, J HS: A Web server to locate periodicities in a sequence. Bioinformatics 1998, 14(8):749-750.
-
(1998)
Bioinformatics
, vol.14
, Issue.8
, pp. 749-750
-
-
Pasquier, C.M.1
Promponas, V.I.2
Varvayannis, N.J.3
-
21
-
-
0036224263
-
Protein sequence comparison based on wavelet transform
-
de Trad CH, Fang Q, Cosic I: Protein sequence comparison based on wavelet transform. Protein Engineering 2002, 15(3):193-202.
-
(2002)
Protein Engineering
, vol.15
, Issue.3
, pp. 193-202
-
-
de Trad, C.H.1
Fang, Q.2
Cosic, I.3
-
22
-
-
0037297509
-
A Novel Approach to the Recognition of Protein Architecture from Sequence Using Fourier Analysis and Neural Networks
-
Shepherd AJ, Gorse D, Thornton JM: A Novel Approach to the Recognition of Protein Architecture from Sequence Using Fourier Analysis and Neural Networks. PROTEINS: Structure, Function, and Genetics 2003, 50:299-302.
-
(2003)
PROTEINS: Structure, Function, and Genetics
, vol.50
, pp. 299-302
-
-
Shepherd, A.J.1
Gorse, D.2
Thornton, J.M.3
-
23
-
-
84874654726
-
Music Database Retrieval Based on Spectral Similarity
-
Stanford University Database Group technical report
-
Cheng Y: Music Database Retrieval Based on Spectral Similarity. Stanford University Database Group technical report 2000:2001-2014.
-
(2000)
, pp. 2001-2014
-
-
Cheng, Y.1
-
24
-
-
84874652086
-
AAindex: Amino Acid Index Database
-
Release 6.0, September
-
AAindex: Amino Acid Index Database, Release 6.0, September 2002 [http://www.genome.ad.jp/dbget/aaindex.html]
-
(2002)
-
-
-
26
-
-
0031008576
-
Hydrophobicity Regained
-
Karplus PA: Hydrophobicity Regained. Protein Science 1997, 6:1302-1307.
-
(1997)
Protein Science
, vol.6
, pp. 1302-1307
-
-
Karplus, P.A.1
-
27
-
-
0037032835
-
The Protein Kinase Complement of the Human Genome
-
Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S: The Protein Kinase Complement of the Human Genome. Science 2002, 298:1912-1934.
-
(2002)
Science
, vol.298
, pp. 1912-1934
-
-
Manning, G.1
Whyte, D.B.2
Martinez, R.3
Hunter, T.4
Sudarsanam, S.5
-
29
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucl Acids Res 2000, 28:235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
30
-
-
0031473847
-
SWISS-MODEL and the Swiss-Pdb-Viewer: An environment for comparative protein modeling
-
Guex N, Peitsch MC: SWISS-MODEL and the Swiss-Pdb-Viewer: An environment for comparative protein modeling. Electrophoresis 1997, 18:1723-2714.
-
(1997)
Electrophoresis
, vol.18
, pp. 1723-2714
-
-
Guex, N.1
Peitsch, M.C.2
-
31
-
-
84885682689
-
Deep View Swiss-PdbViewer
-
Deep View Swiss-PdbViewer [http://www.expasy.org/spdbv/]
-
-
-
-
32
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucl Acids Res 2003, 31:365-370.
-
(2003)
Nucl Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
37
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637.
-
(1983)
Biopolymers
, vol.22
, Issue.12
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|