-
1
-
-
0031576355
-
Do aligned sequences share the same fold?
-
Abagyan, R.A. and Batalov, S. (1997) Do aligned sequences share the same fold? J Mol. Biol., 273, 355-368.
-
(1997)
J Mol. Biol.
, vol.273
, pp. 355-368
-
-
Abagyan, R.A.1
Batalov, S.2
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J Mol. Biol. 215, 403-410.
-
(1990)
J Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
0028289467
-
Issues in searching molecular sequence databases
-
Altschul, S.F., Boguski, M.S., Gish, W. and Wootton, J.C. (1994) Issues in searching molecular sequence databases. [Review] Nature Genet., 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
-
4
-
-
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. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 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
-
5
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.,Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer Jr., E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
6
-
-
0025234646
-
Construction of validated, non-redundant composite protein sequence databases
-
Bleasby, A.J. and Wootton, J.C. (1990) Construction of validated, non-redundant composite protein sequence databases. Protein Eng., 3, 153-159.
-
(1990)
Protein Eng.
, vol.3
, pp. 153-159
-
-
Bleasby, A.J.1
Wootton, J.C.2
-
7
-
-
0028050261
-
OWL - A non-redundant composite protein sequence database
-
Bleasby, A.J., Akrigg, D. and Attwood, T.K. (1994) OWL - a non-redundant composite protein sequence database. Nucleic Acids Res., 22, 3574-3577.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 3574-3577
-
-
Bleasby, A.J.1
Akrigg, D.2
Attwood, T.K.3
-
8
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science (Washington), 253, 164-170.
-
(1991)
Science (Washington)
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
10
-
-
84988046589
-
Gene duplication in H. influenzae
-
Brenner, S., Hubbard, T., Murzin, A. and Chothia, C. (1995) Gene duplication in H. influenzae. Nature, 378, 140.
-
(1995)
Nature
, vol.378
, pp. 140
-
-
Brenner, S.1
Hubbard, T.2
Murzin, A.3
Chothia, C.4
-
11
-
-
0030983386
-
Population statistics of protein structures: Lessons from structural classifications
-
Brenner, S.E., Chothia, C. and Hubbard, T.J. (1997) Population statistics of protein structures: lessons from structural classifications. Curr. Opin. Struct. Biol., 7, 369-376.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 369-376
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
13
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant, S.H. and Lawrence, C.E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins Struct. Funct. Genet., 16, 92-112.
-
(1993)
Proteins Struct. Funct. Genet.
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
14
-
-
0031020765
-
How far can sequences diverge?
-
Chothia, C. and Gerstein, M. (1997) How far can sequences diverge? Nature, 385, 579-581.
-
(1997)
Nature
, vol.385
, pp. 579-581
-
-
Chothia, C.1
Gerstein, M.2
-
15
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia, C. and Lesk, A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
-
(1986)
EMBO J.
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
18
-
-
0029259085
-
Maximum discrimination hidden Markov models of sequence consensus
-
Eddy, S.R., Mitchison, G. and Durbin, R. (1994) Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 9, 9-23.
-
(1994)
J. Comput. Biol.
, vol.9
, pp. 9-23
-
-
Eddy, S.R.1
Mitchison, G.2
Durbin, R.3
-
19
-
-
0031565915
-
A structural census of genomes: Comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure
-
Gerstein, M. (1997) A structural census of genomes: comparing eukaryotic, bacterial and archaeal genomes in terms of protein structure. J. Mol. Biol., 274, 562-576.
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 562-576
-
-
Gerstein, M.1
-
20
-
-
0030339935
-
Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures
-
AAAI Press, Menlo Park, CA
-
Gerstein, M. and Levitt, M. (1996) Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. In Proceedings of the Fourth International. Conference on Intelligent Systems in Molecular Biology. AAAI Press, Menlo Park, CA, pp. 59-67.
-
(1996)
Proceedings of the Fourth International. Conference on Intelligent Systems in Molecular Biology
, pp. 59-67
-
-
Gerstein, M.1
Levitt, M.2
-
21
-
-
0031938039
-
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
-
Gerstein, M. and Levitt, M. (1998) Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci., 7, 445-456.
-
(1998)
Protein Sci.
, vol.7
, pp. 445-456
-
-
Gerstein, M.1
Levitt, M.2
-
22
-
-
0025341905
-
Profile analysis
-
Gribskov, M., Lüthy, R. and Eisenberg, D. (1990) Profile analysis. Methods Enzymol., 183, 146-159.
-
(1990)
Methods Enzymol.
, vol.183
, pp. 146-159
-
-
Gribskov, M.1
Lüthy, R.2
Eisenberg, D.3
-
23
-
-
0028205447
-
Enlarged representative set of protein structures
-
Hobohm, U. and Sander, C. (1994) Enlarged representative set of protein structures. Protein Sci., 3, 522.
-
(1994)
Protein Sci.
, vol.3
, pp. 522
-
-
Hobohm, U.1
Sander, C.2
-
24
-
-
0027092678
-
Selection of representative protein data sets
-
Hobohm, W., Scharf, M., Schneider, R. and Sander, C. (1992) Selection of representative protein data sets. Protein Sci., 1, 409-417.
-
(1992)
Protein Sci.
, vol.1
, pp. 409-417
-
-
Hobohm, W.1
Scharf, M.2
Schneider, R.3
Sander, C.4
-
25
-
-
0030902463
-
New horizons in sequence analysis
-
Hubbard, T.J. (1997) New horizons in sequence analysis. Curr. Opin. Struct. Biol., 7, 190-193.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 190-193
-
-
Hubbard, T.J.1
-
26
-
-
0030792253
-
SCOP: A structural classification of proteins database
-
Hubbard, T.J.P., Murzin, A.G., Brenner, S.E. and Chothia, C. (1997) SCOP: a structural classification of proteins database. Nucleic Acids Res., 25, 236-239.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 236-239
-
-
Hubbard, T.J.P.1
Murzin, A.G.2
Brenner, S.E.3
Chothia, C.4
-
27
-
-
0027305858
-
Alignment and searching for common protein folds using a databank of structural templates
-
Johnson, M.S., Overington, J.P. and Blundell, T.L. (1993) Alignment and searching for common protein folds using a databank of structural templates. J. Mol. Biol., 231, 735-752.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 735-752
-
-
Johnson, M.S.1
Overington, J.P.2
Blundell, T.L.3
-
29
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
30
-
-
0027175241
-
Applications and statistics for multiple high-scoring segments in molecular sequences
-
Karlin, S. and Altschul, S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl Acad. Sci. USA, 90, 5873-5877.
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 5873-5877
-
-
Karlin, S.1
Altschul, S.F.2
-
31
-
-
0028181441
-
Hidden Markov models in computational biology: Applications to protein modelling
-
Krogh, A., Brown, M., Mian, I.S., Sjölander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: applications to protein modelling. J. Mol. Biol., 235, 1501-1531.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.S.3
Sjölander, K.4
Haussler, D.5
-
32
-
-
0032568649
-
A unified statistical framework for sequence comparison and structure comparison
-
Levitt, M. and Gerstein, M. (1998) A unified statistical framework for sequence comparison and structure comparison. Proc. Natl Acad. Sci. USA, 95, 5913-5920.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 5913-5920
-
-
Levitt, M.1
Gerstein, M.2
-
33
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
Lipman, D.J. and Pearson, W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
-
(1985)
Science
, vol.227
, pp. 1435-1441
-
-
Lipman, D.J.1
Pearson, W.R.2
-
34
-
-
0014935646
-
Natural selection and the concept of a protein space
-
Maynard Smith, J. (1970) Natural selection and the concept of a protein space. Nature, 225, 563-564.
-
(1970)
Nature
, vol.225
, pp. 563-564
-
-
Maynard Smith, J.1
-
35
-
-
0028961335
-
SCOP: A structural classification of proteins for the investigation of sequences and structures
-
Murzin, A., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
36
-
-
0028593509
-
Protein superfamilies and domain superfolds
-
Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Protein superfamilies and domain superfolds. Nature, 372, 631-634.
-
(1994)
Nature
, vol.372
, pp. 631-634
-
-
Orengo, C.A.1
Jones, D.T.2
Thornton, J.M.3
-
37
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park, J., Teichmann, S.A., Hubbard, T. and Chothia, C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 349-354
-
-
Park, J.1
Teichmann, S.A.2
Hubbard, T.3
Chothia, C.4
-
38
-
-
0029933671
-
Effective protein sequence comparison
-
Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-259.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 227-259
-
-
Pearson, W.R.1
-
39
-
-
0030776390
-
Identifying distantly related protein sequences
-
Pearson, W.R. (1997) Identifying distantly related protein sequences. Comput. Applic. Biosci., 13, 325-332.
-
(1997)
Comput. Applic. Biosci.
, vol.13
, pp. 325-332
-
-
Pearson, W.R.1
-
40
-
-
0032512799
-
Empirical statistical estimates for sequence similarity searches
-
Pearson, W.R. (1998) Empirical statistical estimates for sequence similarity searches. J. Mol. Biol., 276, 71-84.
-
(1998)
J. Mol. Biol.
, vol.276
, pp. 71-84
-
-
Pearson, W.R.1
-
41
-
-
0023989064
-
Improved tools for biological sequence analysis
-
Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence analysis. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
42
-
-
0031573415
-
Comparison of DNA sequences with protein sequences
-
Pearson, W.R., Wood, T., Zhang, Z. and Miller, W. (1997) Comparison of DNA sequences with protein sequences. Genomics, 46, 24-36.
-
(1997)
Genomics
, vol.46
, pp. 24-36
-
-
Pearson, W.R.1
Wood, T.2
Zhang, Z.3
Miller, W.4
-
43
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
44
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
in press
-
Sonnhammer, J.E., Eddy, S. and Durbin, R. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, in press.
-
(1997)
Proteins
-
-
Sonnhammer, J.E.1
Eddy, S.2
Durbin, R.3
-
45
-
-
0029637588
-
PDBbrowse - A graphics interface to the Brookhaven Protein Data Bank
-
Stampf, D.R., Felder, C.E. and Sussman, J.L. (1995) PDBbrowse - a graphics interface to the Brookhaven Protein Data Bank. Nature, 374, 572-574.
-
(1995)
Nature
, vol.374
, pp. 572-574
-
-
Stampf, D.R.1
Felder, C.E.2
Sussman, J.L.3
-
46
-
-
0028091659
-
Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
-
Tatusov, R.L., Altschul, S.F. and Koonin, E.V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA, 91, 12091-12095.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 12091-12095
-
-
Tatusov, R.L.1
Altschul, S.F.2
Koonin, E.V.3
-
47
-
-
0027496980
-
Weighting in sequence space: A comparison of methods in terms of generalized sequences
-
Vingron, M. and Sibbald, P.R. (1993) Weighting in sequence space: A comparison of methods in terms of generalized sequences. Proc. Natl Acad. Sci. USA, 90, 8777-8781.
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 8777-8781
-
-
Vingron, M.1
Sibbald, P.R.2
-
48
-
-
0004207406
-
-
O'Reilly and Associates, Sebastapol, CA
-
Wall, L., Christiansen, D. and Schwartz, R. (1996) Programming Perl. O'Reilly and Associates, Sebastapol, CA.
-
(1996)
Programming Perl.
-
-
Wall, L.1
Christiansen, D.2
Schwartz, R.3
-
49
-
-
0030987407
-
MultiCoil: A program for predicting two- and three-stranded coiled coils
-
Wolf, E., Kim, P.S. and Berger, B. (1997) MultiCoil: a program for predicting two- and three-stranded coiled coils. Protein Sci., 6, 1179-1189.
-
(1997)
Protein Sci.
, vol.6
, pp. 1179-1189
-
-
Wolf, E.1
Kim, P.S.2
Berger, B.3
-
50
-
-
0001514262
-
Statistics of local complexity in amino acid sequences and sequence databases
-
Wootton, J.C. and Federhen, S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17, 149-163.
-
(1993)
Comput. Chem.
, vol.17
, pp. 149-163
-
-
Wootton, J.C.1
Federhen, S.2
-
51
-
-
0027994453
-
Recognition of related proteins by iterative template refinement (itr)
-
Yi, T.M. and Lander, E.S. (1994) Recognition of related proteins by iterative template refinement (itr). Protein Sci., 3, 1315-1328.
-
(1994)
Protein Sci.
, vol.3
, pp. 1315-1328
-
-
Yi, T.M.1
Lander, E.S.2
-
52
-
-
0029977032
-
Iterative template refinement: Protein-fold prediction using iterative search and hybrid sequence/structure templates
-
Yi, T. and Lander, E.S. (1996) Iterative template refinement: protein-fold prediction using iterative search and hybrid sequence/structure templates. Methods Enzymol., 266, 322-339.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 322-339
-
-
Yi, T.1
Lander, E.S.2
|