-
1
-
-
0020714456
-
Rapid similarity searches of nucleic acid and protein data banks
-
W.J. Wilbur, and D.J. Lipman Rapid similarity searches of nucleic acid and protein data banks Proc Natl Acad Sci USA 80 1983 726 730
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 726-730
-
-
Wilbur, W.J.1
Lipman, D.J.2
-
2
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
D.J. Lipman, and W.R. Pearson Rapid and sensitive protein similarity searches Science 227 1985 1435 1441
-
(1985)
Science
, vol.227
, pp. 1435-1441
-
-
Lipman, D.J.1
Pearson, W.R.2
-
3
-
-
0025183708
-
Basic local alignment search tool
-
S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J Mol Biol 215 1990 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
-
4
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman 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
-
6
-
-
13444304389
-
GenBank
-
D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, and D.L. Wheeler GenBank Nucleic Acids Res 33 2005 D34 D38
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
7
-
-
0020533055
-
Simian sarcoma virus onc gene, v-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor
-
R.F. Doolittle, M.W. Hunkapiller, L.E. Hood, S.G. Devare, K.C. Robbins, S.A. Aaronson, and H.N. Antoniades Simian sarcoma virus onc gene, v-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor Science 221 1983 275 277
-
(1983)
Science
, vol.221
, pp. 275-277
-
-
Doolittle, R.F.1
Hunkapiller, M.W.2
Hood, L.E.3
Devare, S.G.4
Robbins, K.C.5
Aaronson, S.A.6
Antoniades, H.N.7
-
8
-
-
0029785147
-
Mapping the protein universe
-
L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 602
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
10
-
-
0030777303
-
CATH-a hierarchic classification of protein domain structures
-
C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton CATH-a hierarchic classification of protein domain structures Structure 5 1997 1093 1108
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
12
-
-
0013889249
-
An improved method of testing for evolutionary homology
-
W.M. Fitch An improved method of testing for evolutionary homology J Mol Biol 16 1966 9 16
-
(1966)
J Mol Biol
, vol.16
, pp. 9-16
-
-
Fitch, W.M.1
-
13
-
-
0023989064
-
Improved tools for biological sequence comparison
-
W.R. Pearson, and D.J. Lipman Improved tools for biological sequence comparison Proc Natl Acad Sci USA 85 1988 2444 2448
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
14
-
-
0019887799
-
Identification of common molecular subsequences
-
T.F. Smith, and M.S. Waterman 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
-
15
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
S. Karlin, and S.F. Altschul Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes Proc Natl Acad Sci USA 87 1990 2264 2268
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
16
-
-
0002064379
-
Maximum-likelihood-estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
-
R. Mott Maximum-likelihood-estimation of the statistical distribution of Smith-Waterman local sequence similarity scores Bull Math Biol 54 1992 59 75
-
(1992)
Bull Math Biol
, vol.54
, pp. 59-75
-
-
Mott, R.1
-
17
-
-
0032512799
-
Empirical statistical estimates for sequence similarity searches
-
W.R. Pearson Empirical statistical estimates for sequence similarity searches J Mol Biol 276 1998 71 84
-
(1998)
J Mol Biol
, vol.276
, pp. 71-84
-
-
Pearson, W.R.1
-
18
-
-
0035783055
-
On the evolution of protein folds: Are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
-
A.N. Lupas, C.P. Ponting, and R.B. Russell On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world? J Struct Biol 134 2001 191 203
-
(2001)
J Struct Biol
, vol.134
, pp. 191-203
-
-
Lupas, A.N.1
Ponting, C.P.2
Russell, R.B.3
-
19
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
R. Sadreyev, and N.V. Grishin COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance J Mol Biol 326 2003 317 336 A new profile-profile alignment program that extends the PSI-BLAST sequence-profile alignment algorithm is presented. The authors demonstrate its ability to detect remote homologies not detected by PSI-BLAST.
-
(2003)
J Mol Biol
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.V.2
-
20
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
R.C. Edgar, and K. Sjolander A comparison of scoring functions for protein sequence profile alignment Bioinformatics 20 2004 1301 1308
-
(2004)
Bioinformatics
, vol.20
, pp. 1301-1308
-
-
Edgar, R.C.1
Sjolander, K.2
-
21
-
-
4444298729
-
Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
-
T. Ohlson, B. Wallner, and A. Elofsson Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods Proteins 57 2004 188 197
-
(2004)
Proteins
, vol.57
, pp. 188-197
-
-
Ohlson, T.1
Wallner, B.2
Elofsson, A.3
-
22
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
R. Kolodny, P. Koehl, and M. Levitt Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures J Mol Biol 346 2005 1173 1188
-
(2005)
J Mol Biol
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
23
-
-
0242330730
-
Assessment of homology-based predictions in CASP5
-
A. Tramontano, and V. Morea Assessment of homology-based predictions in CASP5 Proteins 53 suppl 6 2003 352 368
-
(2003)
Proteins
, vol.53
, Issue.6 SUPPL.
, pp. 352-368
-
-
Tramontano, A.1
Morea, V.2
-
24
-
-
0242362175
-
Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance
-
C. Venclovas Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance Proteins 53 suppl 6 2003 380 388
-
(2003)
Proteins
, vol.53
, Issue.6 SUPPL.
, pp. 380-388
-
-
Venclovas, C.1
-
25
-
-
0029006770
-
Comparison of methods for searching protein sequence databases
-
W.R. Pearson Comparison of methods for searching protein sequence databases Protein Sci 4 1995 1145 1160
-
(1995)
Protein Sci
, vol.4
, pp. 1145-1160
-
-
Pearson, W.R.1
-
26
-
-
0030935244
-
Using video-oriented instructions to speed up sequence comparison
-
A. Wozniak Using video-oriented instructions to speed up sequence comparison Comput Appl Biosci 13 1997 145 150
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 145-150
-
-
Wozniak, A.1
-
27
-
-
0033743209
-
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
-
T. Rognes, and E. Seeberg Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors Bioinformatics 16 2000 699 706
-
(2000)
Bioinformatics
, vol.16
, pp. 699-706
-
-
Rognes, T.1
Seeberg, E.2
-
28
-
-
0346734129
-
The compositional adjustment of amino acid substitution matrices
-
Y.K. Yu, J.C. Wootton, and S.F. Altschul The compositional adjustment of amino acid substitution matrices Proc Natl Acad Sci USA 100 2003 15688 15693
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15688-15693
-
-
Yu, Y.K.1
Wootton, J.C.2
Altschul, S.F.3
-
30
-
-
0028181441
-
Hidden Markov models in computational biology. Applications to protein modeling
-
A. Krogh, M. Brown, I.S. Mian, K. Sjolander, and D. Haussler Hidden Markov models in computational biology. Applications to protein modeling J Mol Biol 235 1994 1501 1531
-
(1994)
J Mol Biol
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjolander, K.4
Haussler, D.5
-
31
-
-
0029887381
-
Hidden Markov models for sequence analysis: Extension and analysis of the basic method
-
R. Hughey, and A. Krogh Hidden Markov models for sequence analysis: extension and analysis of the basic method Comput Appl Biosci 12 1996 95 107
-
(1996)
Comput Appl Biosci
, vol.12
, pp. 95-107
-
-
Hughey, R.1
Krogh, A.2
-
32
-
-
0031743421
-
Profile hidden Markov models
-
S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
33
-
-
0030941114
-
Embedding strategies for effective use of information from multiple sequence alignments
-
S. Henikoff, and J.G. Henikoff Embedding strategies for effective use of information from multiple sequence alignments Protein Sci 6 1997 698 705
-
(1997)
Protein Sci
, vol.6
, pp. 698-705
-
-
Henikoff, S.1
Henikoff, J.G.2
-
34
-
-
9144257886
-
The Pfam protein families database
-
A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, and E.L. Sonnhammer The Pfam protein families database Nucleic Acids Res 32 2004 D138 D141
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
-
35
-
-
0347125294
-
The SUPERFAMILY database in 2004: Additions and improvements
-
M. Madera, C. Vogel, S.K. Kummerfeld, C. Chothia, and J. Gough The SUPERFAMILY database in 2004: additions and improvements Nucleic Acids Res 32 2004 D235 D239
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Madera, M.1
Vogel, C.2
Kummerfeld, S.K.3
Chothia, C.4
Gough, J.5
-
36
-
-
0038438514
-
IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
-
A.A. Schaffer, Y.I. Wolf, C.P. Ponting, E.V. Koonin, L. Aravind, and S.F. Altschul IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices Bioinformatics 15 1999 1000 1011
-
(1999)
Bioinformatics
, vol.15
, pp. 1000-1011
-
-
Schaffer, A.A.1
Wolf, Y.I.2
Ponting, C.P.3
Koonin, E.V.4
Aravind, L.5
Altschul, S.F.6
-
37
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
A.A. Schaffer, L. Aravind, T.L. Madden, S. Shavirin, J.L. Spouge, Y.I. Wolf, E.V. Koonin, and S.F. Altschul Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements Nucleic Acids Res 29 2001 2994 3005
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
38
-
-
0033574503
-
Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
-
L. Aravind, and E.V. Koonin Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches J Mol Biol 287 1999 1023 1040
-
(1999)
J Mol Biol
, vol.287
, pp. 1023-1040
-
-
Aravind, L.1
Koonin, E.V.2
-
39
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods J Mol Biol 284 1998 1201 1210
-
(1998)
J Mol Biol
, vol.284
, pp. 1201-1210
-
-
Park, J.1
Karplus, K.2
Barrett, C.3
Hughey, R.4
Haussler, D.5
Hubbard, T.6
Chothia, C.7
-
40
-
-
0029789461
-
Searching databases of conserved sequence regions by aligning protein multiple-alignments
-
S. Pietrokovski Searching databases of conserved sequence regions by aligning protein multiple-alignments Nucleic Acids Res 24 1996 3836 3845
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 3836-3845
-
-
Pietrokovski, S.1
-
41
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
L. Rychlewski, L. Jaroszewski, W. Li, and A. Godzik Comparison of sequence profiles. Strategies for structural predictions using sequence information Protein Sci 9 2000 232 241
-
(2000)
Protein Sci
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.3
Godzik, A.4
-
42
-
-
0036307493
-
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
-
G. Yona, and M. Levitt Within the twilight zone: a sensitive profile-profile comparison tool based on information theory J Mol Biol 315 2002 1257 1275
-
(2002)
J Mol Biol
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
-
43
-
-
2942544229
-
COACH: Profile-profile alignment of protein families using hidden Markov models
-
R.C. Edgar, and K. Sjolander COACH: profile-profile alignment of protein families using hidden Markov models Bioinformatics 20 2004 1309 1318
-
(2004)
Bioinformatics
, vol.20
, pp. 1309-1318
-
-
Edgar, R.C.1
Sjolander, K.2
-
44
-
-
0141634362
-
Profile-profile comparisons by COMPASS predict intricate homologies between protein families
-
R.I. Sadreyev, D. Baker, and N.V. Grishin Profile-profile comparisons by COMPASS predict intricate homologies between protein families Protein Sci 12 2003 2262 2272
-
(2003)
Protein Sci
, vol.12
, pp. 2262-2272
-
-
Sadreyev, R.I.1
Baker, D.2
Grishin, N.V.3
-
45
-
-
0345827718
-
Using evolutionary information for the query and target improves fold recognition
-
B. Wallner, H. Fang, T. Ohlson, J. Frey-Skott, and A. Elofsson Using evolutionary information for the query and target improves fold recognition Proteins 54 2004 342 350
-
(2004)
Proteins
, vol.54
, pp. 342-350
-
-
Wallner, B.1
Fang, H.2
Ohlson, T.3
Frey-Skott, J.4
Elofsson, A.5
-
46
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
I.N. Shindyalov, and P.E. Bourne Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng 11 1998 739 747
-
(1998)
Protein Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
47
-
-
0032568649
-
A unified statistical framework for sequence comparison and structure comparison
-
M. Levitt, and M. Gerstein A unified statistical framework for sequence comparison and structure comparison Proc Natl Acad Sci USA 95 1998 5913 5920
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 5913-5920
-
-
Levitt, M.1
Gerstein, M.2
-
48
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
S.E. Brenner, C. Chothia, and T.J. Hubbard Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships Proc Natl Acad Sci USA 95 1998 6073 6078
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
49
-
-
0345983651
-
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison
-
R.E. Green, and S.E. Brenner Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison Proc IEEE 90 2002 1834 1847
-
(2002)
Proc IEEE
, vol.90
, pp. 1834-1847
-
-
Green, R.E.1
Brenner, S.E.2
-
50
-
-
0346734106
-
Detection of homologous proteins by an intermediate sequence search
-
B. John, and A. Sali Detection of homologous proteins by an intermediate sequence search Protein Sci 13 2004 54 62
-
(2004)
Protein Sci
, vol.13
, pp. 54-62
-
-
John, B.1
Sali, A.2
-
51
-
-
1342289274
-
Sensitivity and selectivity in protein structure comparison
-
M.L. Sierk, and W.R. Pearson Sensitivity and selectivity in protein structure comparison Protein Sci 13 2004 773 785 The first attempt to assess the accuracy of the statistical estimates provided by various structure alignment programs, in terms of detecting homologous domains in the CATH database. The authors demonstrate that many structure alignment programs overestimate the significance of structural similarities when searching the database for potential homologs.
-
(2004)
Protein Sci
, vol.13
, pp. 773-785
-
-
Sierk, M.L.1
Pearson, W.R.2
-
52
-
-
2442663920
-
Scoring profile-to-profile sequence alignments
-
G. Wang, and R.L. Dunbrack Jr. Scoring profile-to-profile sequence alignments Protein Sci 13 2004 1612 1626 A systematic assessment of different statistical models for comparing sequence profiles. The authors demonstrate that there is little difference between scoring systems once gap scores are optimized.
-
(2004)
Protein Sci
, vol.13
, pp. 1612-1626
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
53
-
-
0036796379
-
A comparison of profile hidden Markov model procedures for remote homology detection
-
M. Madera, and J. Gough A comparison of profile hidden Markov model procedures for remote homology detection Nucleic Acids Res 30 2002 4321 4328
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4321-4328
-
-
Madera, M.1
Gough, J.2
-
54
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
W.R. Pearson Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms Genomics 11 1991 635 650
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
|