-
1
-
-
0023305986
-
Knowledge-based prediction of protein structures and the design of novel molecules
-
Blundell TL, Sibanda BL, Sternberg MJE, Thornton JM. Knowledge-based prediction of protein structures and the design of novel molecules. Nature 1987;326:347-352.
-
(1987)
Nature
, vol.326
, pp. 347-352
-
-
Blundell, T.L.1
Sibanda, B.L.2
Sternberg, M.J.E.3
Thornton, J.M.4
-
2
-
-
0025287330
-
Comparative modeling methods: Application to the family of the mammalian serine proteases
-
Greer J. Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins 1990;7:317-334.
-
(1990)
Proteins
, vol.7
, pp. 317-334
-
-
Greer, J.1
-
3
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Šali, A.1
Blundell, T.L.2
-
4
-
-
0014693695
-
A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme
-
Browne WJ, North AC, Phillips DC. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J Mol Biol 1969;42:65-86.
-
(1969)
J Mol Biol
, vol.42
, pp. 65-86
-
-
Browne, W.J.1
North, A.C.2
Phillips, D.C.3
-
5
-
-
0019028066
-
Model for haptoglobin heavy chain based upon structural homology
-
Greer J. Model for haptoglobin heavy chain based upon structural homology. Proc Natl Acad Sci USA 1980;77:3393-3397.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 3393-3397
-
-
Greer, J.1
-
6
-
-
0001433241
-
Knowledge based modeling of homologous proteins, part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
-
Sutcliffe MJ, Haneef I, Carney D, Blundell TL. Knowledge based modeling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Prot Eng 1987;5:377-384.
-
(1987)
Prot Eng
, vol.5
, pp. 377-384
-
-
Sutcliffe, M.J.1
Haneef, I.2
Carney, D.3
Blundell, T.L.4
-
7
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 1970;48:443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
8
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
9
-
-
0025341237
-
Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
-
Bowie JU, Clarke ND, Pabo CO, Sauer RT. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins 1990;7:257-264.
-
(1990)
Proteins
, vol.7
, pp. 257-264
-
-
Bowie, J.U.1
Clarke, N.D.2
Pabo, C.O.3
Sauer, R.T.4
-
10
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models
-
Hendlich M, Lackner P, Weitckus S, Flöckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. J Mol Biol 1990;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Flöckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
11
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
12
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
13
-
-
0029874551
-
Protein fold recognition using sequencederived predictions
-
Fischer D, Eisenberg D. Protein fold recognition using sequencederived predictions. Prot Sci 1996;5:947-955.
-
(1996)
Prot Sci
, vol.5
, pp. 947-955
-
-
Fischer, D.1
Eisenberg, D.2
-
14
-
-
0031576361
-
Intermediate sequences increase the detection of homology between sequences
-
Park J, Teichmann SA, Hubbard T, Chothia C. Intermediate sequences increase the detection of homology between sequences. J Mol Biol 1997;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
-
15
-
-
0031762837
-
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
-
Gerstein M. Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics 1998;14:707-714.
-
(1998)
Bioinformatics
, vol.14
, pp. 707-714
-
-
Gerstein, M.1
-
16
-
-
0032940341
-
Combining sensitive database searched with multiple intermediates to detect distant homologues
-
Salamov AA, Suwa M, Orengo CA, Swindells MB. Combining sensitive database searched with multiple intermediates to detect distant homologues. Prot Eng 1999;12:95-100.
-
(1999)
Prot Eng
, vol.12
, pp. 95-100
-
-
Salamov, A.A.1
Suwa, M.2
Orengo, C.A.3
Swindells, M.B.4
-
17
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999;12:85-94.
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
19
-
-
0032568596
-
Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
-
Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998;95:6073-6078.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 6073-6078
-
-
Brenner, S.E.1
Chothia, C.2
Hubbard, T.J.3
-
20
-
-
0025272240
-
Rapid and sensitive sequence comparison with FASTP and FASTA
-
Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Meth Enz 1990;183:63-98.
-
(1990)
Meth Enz
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
21
-
-
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
-
22
-
-
0029889221
-
Local alignment statistics
-
Altschul SF, Gish W. Local alignment statistics. Meth Enz 1996;266:460-480.
-
(1996)
Meth Enz
, vol.266
, pp. 460-480
-
-
Altschul, S.F.1
Gish, W.2
-
23
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
24
-
-
0032509105
-
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
-
Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J Mol Biol 1998;284:1201-1210.
-
(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
-
25
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
26
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton J. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
-
(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.6
-
27
-
-
0030582739
-
Significant improvement in accuracy of multiple sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh O. Significant improvement in accuracy of multiple sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 1996;264:823-838.
-
(1996)
J Mol Biol
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
28
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucl Acids Res 1999;27: 2682-2690.
-
(1999)
Nucl Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
29
-
-
0023518540
-
A strategy for the rapid multiple alignment of protein sequences: Confidence levels from tertiary structure comparisons
-
Barton GJ, Sternberg MJE. A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. J Mol Biol 1987;198:327-337.
-
(1987)
J Mol Biol
, vol.198
, pp. 327-337
-
-
Barton, G.J.1
Sternberg, M.J.E.2
-
30
-
-
0029921425
-
A surface of minimum area metric for the structural comparison of proteins
-
Falicov A, Cohen FE. A surface of minimum area metric for the structural comparison of proteins. J Mol Biol 1996;258:871-892.
-
(1996)
J Mol Biol
, vol.258
, pp. 871-892
-
-
Falicov, A.1
Cohen, F.E.2
-
31
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Prot Engl 1998;11:739-747.
-
(1998)
Prot Engl
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
32
-
-
0030628304
-
Hierarchical protein structure superposition using both secondary structure and atomic representations
-
Singh AP, Brutlag DL. Hierarchical protein structure superposition using both secondary structure and atomic representations. Ismb 1997;5:284-293.
-
(1997)
Ismb
, vol.5
, pp. 284-293
-
-
Singh, A.P.1
Brutlag, D.L.2
-
33
-
-
0028871926
-
Dali: A network tool for protein structure comparison
-
Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 478-480
-
-
Holm, L.1
Sander, C.2
-
34
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
-
Russell RB, Barton GJ. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992;14:309-323.
-
(1992)
Proteins
, vol.14
, pp. 309-323
-
-
Russell, R.B.1
Barton, G.J.2
-
35
-
-
0029948001
-
SSAP: Sequential structure alignment program for protein structure comparison
-
Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Meth Enz 1996;266:617-635.
-
(1996)
Meth Enz
, vol.266
, pp. 617-635
-
-
Orengo, C.A.1
Taylor, W.R.2
-
36
-
-
0030334647
-
Optimum superimposition of protein structures: Ambiguities and implications
-
Feng Z, Sippl MJ. Optimum superimposition of protein structures: ambiguities and implications. Fold Des 1996;1:123-132.
-
(1996)
Fold Des
, vol.1
, pp. 123-132
-
-
Feng, Z.1
Sippl, M.J.2
-
37
-
-
0029982530
-
The structural alignment between two proteins: Is there a unique answer?
-
Godzik A. The structural alignment between two proteins: is there a unique answer? Prot Sci 1996;5:1325-1338.
-
(1996)
Prot Sci
, vol.5
, pp. 1325-1338
-
-
Godzik, A.1
-
38
-
-
0028051828
-
Derivation of rules for comparative protein modeling from a database of protein structure alignments
-
Šali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Prot Sci 1994;3:1582-1596.
-
(1994)
Prot Sci
, vol.3
, pp. 1582-1596
-
-
Šali, A.1
Overington, J.P.2
-
39
-
-
0027210418
-
Optimal alignment between groups of sequences and its application to multiple sequence alignment
-
Gotoh O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci 1993;9:361-370.
-
(1993)
Comput Appl Biosci
, vol.9
, pp. 361-370
-
-
Gotoh, O.1
-
40
-
-
0028041177
-
Further improvement in methods of group-to-group sequence alignment with generalized profile operations
-
Gotoh O. Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comput Appl Biosci 1994;10:379-387.
-
(1994)
Comput Appl Biosci
, vol.10
, pp. 379-387
-
-
Gotoh, O.1
-
41
-
-
0028787980
-
A weighting system and algorithm for aligning many phylogenetically related sequences
-
Gotoh O. A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci 1995;11: 543-551.
-
(1995)
Comput Appl Biosci
, vol.11
, pp. 543-551
-
-
Gotoh, O.1
-
42
-
-
0029174347
-
Multiple alignment using hidden Markov models
-
Eddy SR. Multiple alignment using hidden Markov models. Ismb 1995;3:114-120.
-
(1995)
Ismb
, vol.3
, pp. 114-120
-
-
Eddy, S.R.1
-
43
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
Holm L, Sander C. Touring protein fold space with Dali/FSSP. Nucl Acids Res 1998;26:316-319.
-
(1998)
Nucl Acids Res
, vol.26
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
44
-
-
0032940544
-
SCOP: A structural classification of proteins database
-
Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C. SCOP: a structural classification of proteins database. Nucl Acids Res 1999;27:254-256.
-
(1999)
Nucl Acids Res
, vol.27
, pp. 254-256
-
-
Hubbard, T.J.1
Ailey, B.2
Brenner, S.E.3
Murzin, A.G.4
Chothia, C.5
-
45
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986;5:823-826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
46
-
-
0029918694
-
The FSSP database: Fold classification based on structure-structure alignment of proteins
-
Holm L, Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucl Acids Res 1996;24: 206-209.
-
(1996)
Nucl Acids Res
, vol.24
, pp. 206-209
-
-
Holm, L.1
Sander, C.2
-
47
-
-
0026511848
-
A data bank merging related protein structures and sequences
-
Pascarella S, Argos P. A data bank merging related protein structures and sequences. Prot Eng 1992;5:121-137.
-
(1992)
Prot Eng
, vol.5
, pp. 121-137
-
-
Pascarella, S.1
Argos, P.2
-
48
-
-
0031938039
-
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
-
Gerstein M, Levitt M. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Prot Sci 1998;7:445-456.
-
(1998)
Prot Sci
, vol.7
, pp. 445-456
-
-
Gerstein, M.1
Levitt, M.2
-
49
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment 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 alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994;22:4673-4680.
-
(1994)
Nucl Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
50
-
-
0029976603
-
Using CLUSTAL for multiple sequence alignments
-
Huggins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Meth Enz 1996;266:383-402.
-
(1996)
Meth Enz
, vol.266
, pp. 383-402
-
-
Huggins, D.G.1
Thompson, J.D.2
Gibson, T.J.3
-
51
-
-
0032540845
-
Homology-based fold predictions for Mycoplasma genitalium proteins
-
Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. Homology-based fold predictions for Mycoplasma genitalium proteins. J Mol Biol 1998;280:323-326.
-
(1998)
J Mol Biol
, vol.280
, pp. 323-326
-
-
Huynen, M.1
Doerks, T.2
Eisenhaber, F.3
Orengo, C.4
Sunyaev, S.5
Yuan, Y.6
Bork, P.7
-
52
-
-
0032919371
-
Protein folds and families: Sequence and structure alignments
-
Holm L, Sander C. Protein folds and families: sequence and structure alignments. Nucl Acids Res 1999;27:244-247.
-
(1999)
Nucl Acids Res
, vol.27
, pp. 244-247
-
-
Holm, L.1
Sander, C.2
-
53
-
-
0032613301
-
Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL
-
Dunbrack RL, Jr. Comparative modeling of CASP3 targets using PSI-BLAST and SCWRL. Protein (Suppl) 1999;3:81-87.
-
(1999)
Protein
, vol.3
, Issue.SUPPL.
, pp. 81-87
-
-
Dunbrack R.L., Jr.1
-
54
-
-
0032922003
-
MMDB: Entrez's 3D structure database
-
Marchler-Bauer A, Addess KJ, Chappey C, Geer L, Madej T, Matsuo Y, Wang Y, Bryant SH. MMDB: Entrez's 3D structure database. Nucl Acids Res 1999;27:240-243.
-
(1999)
Nucl Acids Res
, vol.27
, pp. 240-243
-
-
Marchler-Bauer, A.1
Addess, K.J.2
Chappey, C.3
Geer, L.4
Madej, T.5
Matsuo, Y.6
Wang, Y.7
Bryant, S.H.8
-
55
-
-
0030724017
-
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
-
Fischer D, Eisenberg D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 1997;94:11929-11934.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 11929-11934
-
-
Fischer, D.1
Eisenberg, D.2
-
56
-
-
0032942295
-
Genome analysis: Assigning protein coding regions to three-dimensional structures
-
Salamov AA, Suwa M, Orengo CA, Swindells MB. Genome analysis: assigning protein coding regions to three-dimensional structures. Prot Sci 1999;8:771-777.
-
(1999)
Prot Sci
, vol.8
, pp. 771-777
-
-
Salamov, A.A.1
Suwa, M.2
Orengo, C.A.3
Swindells, M.B.4
-
57
-
-
0031844330
-
Fold and function predictions for Mycoplasma genitalium proteins
-
Rychlewski L, Zhang B, Godzik A. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 1998;3:229-238.
-
(1998)
Fold Des
, vol.3
, pp. 229-238
-
-
Rychlewski, L.1
Zhang, B.2
Godzik, A.3
-
58
-
-
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
-
59
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of database programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of database programs. Nucl Acids Res 1997;25:3389-3402.
-
(1997)
Nucl Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
60
-
-
0028501914
-
Non-globular domains in protein sequences: Automated segmentation using complexity measures
-
Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994;18:269-285.
-
(1994)
Comput Chem
, vol.18
, pp. 269-285
-
-
Wootton, J.C.1
-
61
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
|