-
1
-
-
0020649886
-
Establishing homologies in protein sequences
-
Dayhoff, M.O., Barker, W.C. & Hunt, L.T. (1983). Establishing homologies in protein sequences. Methods Enzymol. 91, 254.
-
(1983)
Methods Enzymol.
, vol.91
, pp. 254
-
-
Dayhoff, M.O.1
Barker, W.C.2
Hunt, L.T.3
-
2
-
-
0028047892
-
Sequence alignment and penalty choices. Review of concepts, case studies and implications
-
Vingron, M. & Waterman, M.S. (1994). Sequence alignment and penalty choices. Review of concepts, case studies and implications. J. Mol. Biol. 235(1), 1-12.
-
(1994)
J. Mol. Biol.
, vol.235
, Issue.1
, pp. 1-12
-
-
Vingron, M.1
Waterman, M.S.2
-
3
-
-
0020972771
-
Protein and nucleic acid sequence database systems
-
Orcutt, B.C., George, D.G. & Dayhoff, M.O. (1983). Protein and nucleic acid sequence database systems. Annu. Rev. Biochem. Biophys. 12, 419-441.
-
(1983)
Annu. Rev. Biochem. Biophys.
, vol.12
, pp. 419-441
-
-
Orcutt, B.C.1
George, D.G.2
Dayhoff, M.O.3
-
4
-
-
0023375315
-
Profile analysis: Detection of distantly related proteins
-
Gribskov, M., McLachlan, A.D. & Eisenberg, D. (1987). Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84(13), 4355-4388.
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, Issue.13
, pp. 4355-4388
-
-
Gribskov, M.1
McLachlan, A.D.2
Eisenberg, D.3
-
5
-
-
0028304890
-
Recognition of distantly related proteins through energy calculations
-
Abagyan, R., Frishman, D. & Argos, P. (1994). Recognition of distantly related proteins through energy calculations. Proteins 19(2), 132-140.
-
(1994)
Proteins
, vol.19
, Issue.2
, pp. 132-140
-
-
Abagyan, R.1
Frishman, D.2
Argos, P.3
-
6
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J.U., Lüthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science 253, 164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
7
-
-
0027318317
-
An empirical energy function for threading protein sequences through the folding motif
-
Bryant, S.H. & Lawrence, C.E. (1993). An empirical energy function for threading protein sequences through the folding motif. Proteins 16(1), 92-112.
-
(1993)
Proteins
, vol.16
, Issue.1
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
8
-
-
14744303317
-
New programs for protein tertiary structure prediction
-
Fetrow, J.S. & Bryant, S.H. (1993). New programs for protein tertiary structure prediction. Biotechnology 11 (4), 479-484.
-
(1993)
Biotechnology
, vol.11
, Issue.4
, pp. 479-484
-
-
Fetrow, J.S.1
Bryant, S.H.2
-
9
-
-
0028802198
-
Progress in fold recognition
-
Flöckner, H., Braxenthaler, M., Lackner, P., Jaritz, M., Ortner, M. & Sippl, M.J. (1995). Progress in fold recognition. Proteins 23(3), 376-386.
-
(1995)
Proteins
, vol.23
, Issue.3
, pp. 376-386
-
-
Flöckner, H.1
Braxenthaler, M.2
Lackner, P.3
Jaritz, M.4
Ortner, M.5
Sippl, M.J.6
-
10
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik, A., Kolinski, A. & Skolnick, J. (1992). Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227, 227-238.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
11
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D.T., Taylor, W.R. & 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
-
12
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify sequence-structure matches
-
Kocher, J.-P.A., Rooman, M.J. & Wodak, S.J. (1994). Factors influencing the ability of knowledge-based potentials to identify sequence-structure matches. J. Mol. Biol. 235, 1598-1613.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1598-1613
-
-
Kocher, J.-P.A.1
Rooman, M.J.2
Wodak, S.J.3
-
13
-
-
0027302043
-
Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles from three-dimensional structures
-
Ouzounis, C., Sander, C., Scharf, M. & Schneider, R. (1993). Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles from three-dimensional structures. J. Mol. Biol. 232(3), 805-825.
-
(1993)
J. Mol. Biol.
, vol.232
, Issue.3
, pp. 805-825
-
-
Ouzounis, C.1
Sander, C.2
Scharf, M.3
Schneider, R.4
-
14
-
-
0026447086
-
Extracting information from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions
-
Rooman, M.J., Kocher, J.-P.A. & Wodak, S.J. (1992). Extracting information from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 31, 10226-10238.
-
(1992)
Biochemistry
, vol.31
, pp. 10226-10238
-
-
Rooman, M.J.1
Kocher, J.-P.A.2
Wodak, S.J.3
-
15
-
-
0028330013
-
The three-dimensional profile method using residue preferences as a continuous function of residue environment
-
Zhang, K.Y.J. & Eisenberg, D. (1994). The three-dimensional profile method using residue preferences as a continuous function of residue environment. Protein Sci. 3, 687-695.
-
(1994)
Protein Sci.
, vol.3
, pp. 687-695
-
-
Zhang, K.Y.J.1
Eisenberg, D.2
-
16
-
-
0028579433
-
Protein structural similarities predicted by a sequence-structure compatibility method
-
Matsuo, Y. & Nishikawa, K. (1994). Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 3, 2055-2063.
-
(1994)
Protein Sci.
, vol.3
, pp. 2055-2063
-
-
Matsuo, Y.1
Nishikawa, K.2
-
17
-
-
0027458885
-
Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold
-
Wilmanns, M. & Eisenberg, D. (1993). Three-dimensional profiles from residue-pair preferences: identification of sequences with β/α-barrel fold. Proc. Natl. Acad. Sci. USA 90, 1379-1383.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 1379-1383
-
-
Wilmanns, M.1
Eisenberg, D.2
-
18
-
-
0028886967
-
Inverse protein folding by the residue pair preference profile method: Estimating the correctness of alignments of structurally compatible sequences
-
Wilmanns, M. & Eisenberg, D. (1995). Inverse protein folding by the residue pair preference profile method: estimating the correctness of alignments of structurally compatible sequences. Protein Eng. 8, 627-639.
-
(1995)
Protein Eng.
, vol.8
, pp. 627-639
-
-
Wilmanns, M.1
Eisenberg, D.2
-
19
-
-
0027994453
-
Recognition of related proteins by iterative template refinement (IRT)
-
Yi, T.M. & Lander, E.S. (1994). Recognition of related proteins by iterative template refinement (IRT). Protein Sci. 3(8), 1315-1328.
-
(1994)
Protein Sci.
, vol.3
, Issue.8
, pp. 1315-1328
-
-
Yi, T.M.1
Lander, E.S.2
-
20
-
-
0029874551
-
Protein fold recognition using sequence-derived predictions
-
Fischer, D. & Eisenberg, D. (1996). Protein fold recognition using sequence-derived predictions. Protein Sci. 5, 947-955.
-
(1996)
Protein Sci.
, vol.5
, pp. 947-955
-
-
Fischer, D.1
Eisenberg, D.2
-
21
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. & Henikoff, J. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad Sci. USA 89, 10915-10919.
-
(1992)
Proc. Natl. Acad Sci. USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.2
-
22
-
-
0028279408
-
Analysis of aminoacid substitution during divergent evolution: The 400 by 400 dipeptide substitution matrix
-
Gonnet, G.H., Cohen, MA & Benner, S.A. (1994). Analysis of aminoacid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. Biochem. Biophys. Res. Commun. 199(2), 489-496.
-
(1994)
Biochem. Biophys. Res. Commun.
, vol.199
, Issue.2
, pp. 489-496
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
23
-
-
33645855544
-
-
Genetics Computer Group, Madison, Wisconsin, USA
-
Genetics Computer Group. (1982). GCG: Version 8.0. Genetics Computer Group, Madison, Wisconsin, USA.
-
(1982)
GCG: Version 8.0
-
-
-
24
-
-
0025008445
-
Identification of native folds amongst a large number of incorrect models. the calculation of low energy conformations from potentials of mean force
-
Hendlich, M., et al., & Sippl, M.J. (1990). Identification of native folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Sippl, M.J.2
-
25
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
Lathrop, R.H. (1994). The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7(9), 1059-1068.
-
(1994)
Protein Eng.
, vol.7
, Issue.9
, pp. 1059-1068
-
-
Lathrop, R.H.1
-
26
-
-
0019764298
-
Comparative biosequence metrics
-
Smith, T.F., Waterman, M.S. & Fitch, W.M. (1981). Comparative biosequence metrics. J. Mol. Evol. 18(1), 38-46.
-
(1981)
J. Mol. Evol.
, vol.18
, Issue.1
, pp. 38-46
-
-
Smith, T.F.1
Waterman, M.S.2
Fitch, W.M.3
-
27
-
-
0030310317
-
Assessing the performance of fold recognition methods by means of a comprehensive benchmark
-
Hunter, L., Klein, T.E., eds, World Scientific Publishers, New Jersey
-
Fischer, D., Elofsson, A., Rice, D.W. & Eisenberg, D. (1996). Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In Pacific Symposium on Biocomputing '96. (Hunter, L., Klein, T.E., eds), pp. 300-318, World Scientific Publishers, New Jersey.
-
(1996)
Pacific Symposium on Biocomputing '96
, pp. 300-318
-
-
Fischer, D.1
Elofsson, A.2
Rice, D.W.3
Eisenberg, D.4
-
28
-
-
0029006770
-
Comparison of methods for searching protein databases
-
Pearson, W.R. (1995). Comparison of methods for searching protein databases. Protein Sci. 4, 1145-1160.
-
(1995)
Protein Sci.
, vol.4
, pp. 1145-1160
-
-
Pearson, W.R.1
-
29
-
-
0029564871
-
A 3D sequence-independent representation of the protein data bank
-
Fischer, D., Tsai, C.J., Nussinov, R. & Wolfson, H. (1995). A 3D sequence-independent representation of the protein data bank. Protein Eng. 8(10), 981-997.
-
(1995)
Protein Eng.
, vol.8
, Issue.10
, pp. 981-997
-
-
Fischer, D.1
Tsai, C.J.2
Nussinov, R.3
Wolfson, H.4
-
30
-
-
0021100781
-
Statistical characterization of nucleic acid sequence functional domains
-
Smith, T.F., Waterman, M.S. & Sadler, J.R. (1983). Statistical characterization of nucleic acid sequence functional domains. Nucleic Acids Res. 11(7), 2205-2220.
-
(1983)
Nucleic Acids Res.
, vol.11
, Issue.7
, pp. 2205-2220
-
-
Smith, T.F.1
Waterman, M.S.2
Sadler, J.R.3
-
31
-
-
0021760095
-
Algorithms for restriction map comparisons
-
Waterman, M.S., Smith, T.F. & Katcher, H.L. (1984). Algorithms for restriction map comparisons. Nucleic Acids Res. 11 (12), 237-242.
-
(1984)
Nucleic Acids Res.
, vol.11
, Issue.12
, pp. 237-242
-
-
Waterman, M.S.1
Smith, T.F.2
Katcher, H.L.3
-
32
-
-
0028328263
-
An evolutionary approach to folding α-helical proteins that uses sequence information and an empirical guiding fitness function
-
Bowie, J.U. & Eisenberg, D. (1994). An evolutionary approach to folding α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc. Natl. Acad. Sci. USA 91(10), 4436-4440.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, Issue.10
, pp. 4436-4440
-
-
Bowie, J.U.1
Eisenberg, D.2
-
33
-
-
0029085037
-
Local moves: An efficient algorithm for simulation of protein folding
-
Elofsson, A., Le Grand, S.M. & Eisenberg, D. (1995). Local moves: an efficient algorithm for simulation of protein folding. Proteins 23, 73-82.
-
(1995)
Proteins
, vol.23
, pp. 73-82
-
-
Elofsson, A.1
Le Grand, S.M.2
Eisenberg, D.3
-
34
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247(4), 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
35
-
-
0028205447
-
Enlarged representative set of proteins
-
Hobohm, U. & Sander, C. (1994). Enlarged representative set of proteins. Protein Sci. 3, 522-524.
-
(1994)
Protein Sci.
, vol.3
, pp. 522-524
-
-
Hobohm, U.1
Sander, C.2
-
36
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B. & Richards, F.M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55(3), 379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, Issue.3
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
37
-
-
0027650879
-
Boltzmann's principle, knowledge based mean fields and protein folding
-
Sippl, M.J. (1993). Boltzmann's principle, knowledge based mean fields and protein folding. J. Comput. Aided Mol. Des. 7, 473-501.
-
(1993)
J. Comput. Aided Mol. Des.
, vol.7
, pp. 473-501
-
-
Sippl, M.J.1
|