-
1
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle T-F, Williams GJ, Meyer, EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M, The Protein Data Bank: A computer-based archival file for macromolecular structures, J Mol Biol 112(3):535-542, 1977.
-
(1977)
J Mol Biol
, vol.112
, Issue.3
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.-F.2
Williams, G.J.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
2
-
-
44049083028
-
-
Zhu B, On the complexity of protein local structure alignment under the discrete Frechet distance, arXiv:0709.0677, 2007.
-
Zhu B, On the complexity of protein local structure alignment under the discrete Frechet distance, arXiv:0709.0677, 2007.
-
-
-
-
3
-
-
37849047019
-
Finding compact structural motifs
-
Qian J, Li S, Bu D, Li M, Xu J, Finding compact structural motifs, Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), pp. 142-149, 2007.
-
(2007)
Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07)
, pp. 142-149
-
-
Qian, J.1
Li, S.2
Bu, D.3
Li, M.4
Xu, J.5
-
4
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson WR, Flexible sequence similarity searching with the FASTA3 program package, Methods Mol Biol 132:185-219, 2000.
-
(2000)
Methods Mol Biol
, vol.132
, pp. 185-219
-
-
Pearson, W.R.1
-
5
-
-
17644392830
-
A protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J, TM-align: A protein structure alignment algorithm based on the TM-score, Nucleic Acids Res 33(7):2302-2309, 2005.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
align, T.3
-
6
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm L, Sander C, Protein structure comparison by alignment of distance matrices, J Mol Biol 233(1):123-138, 1993.
-
(1993)
J Mol Biol
, vol.233
, Issue.1
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
7
-
-
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, Protein Eng 11(9):739-747, 1998.
-
(1998)
Protein Eng
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
8
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Pt 1
-
Krissinel E, Henrick K, Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2256-2268, 2004.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, Issue.PART 12
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
9
-
-
84863022204
-
Protein structure-structure alignment with discrete Frechet distance
-
Imperial College Press, London, pp
-
Jiang M, Xu Y, Zhu B, Protein structure-structure alignment with discrete Frechet distance, in Proceedings of the 5th Asia Pacific Bioinformatics Conference (APBC'07), Imperial College Press, London, pp. 131-141, 2007.
-
(2007)
Proceedings of the 5th Asia Pacific Bioinformatics Conference (APBC'07)
, pp. 131-141
-
-
Jiang, M.1
Xu, Y.2
Zhu, B.3
-
10
-
-
3242888280
-
ProteinDBS: A real-time retrieval system for protein structure comparison
-
Web Server issue:W572-W575
-
Shyu C-R, Chi P-H, Scott G, Xu D, ProteinDBS: A real-time retrieval system for protein structure comparison, Nucleic Acids Res 32 Web Server issue):W572-W575, 2004.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Shyu, C.-R.1
Chi, P.-H.2
Scott, G.3
Xu, D.4
-
11
-
-
1842450688
-
FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions
-
Shatsky M, Nussinov R, Wolfson HJ, FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions, J Comput Biol 11(1):83-106, 2004.
-
(2004)
J Comput Biol
, vol.11
, Issue.1
, pp. 83-106
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.J.3
-
12
-
-
3242887315
-
FATCAT: A web server for flexible structure comparison and structure similarity searching
-
Web Server issue:W582-W585
-
Ye Y, Godzik A, FATCAT: A web server for flexible structure comparison and structure similarity searching, Nucleic Acids Res 32(Web Server issue):W582-W585, 2004.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Ye, Y.1
Godzik, A.2
-
13
-
-
0037422619
-
Automatic classification of protein structure by using Gauss integrals
-
Rogen P, Fain B, Automatic classification of protein structure by using Gauss integrals, Proc Natl Acad Sci USA 100(1):119-124, 2003.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.1
, pp. 119-124
-
-
Rogen, P.1
Fain, B.2
-
14
-
-
0242585484
-
A new family of global protein shape descriptors
-
Rogen P, Bohr H, A new family of global protein shape descriptors, Math Biosci 182(2):167-181, 2003.
-
(2003)
Math Biosci
, vol.182
, Issue.2
, pp. 167-181
-
-
Rogen, P.1
Bohr, H.2
-
15
-
-
27544483936
-
CHORAL: A differential geometry approach to the prediction of the cores of protein structures
-
Montalvao RW, Smith RE, Lovell SC, Blundell TL, CHORAL: A differential geometry approach to the prediction of the cores of protein structures, Bioinformatics 21(19):3719-3725, 2005.
-
(2005)
Bioinformatics
, vol.21
, Issue.19
, pp. 3719-3725
-
-
Montalvao, R.W.1
Smith, R.E.2
Lovell, S.C.3
Blundell, T.L.4
-
16
-
-
33748374227
-
Structure alignment based on coding of local geometric measures
-
Chang PL, Rinne AW, Dewey TG, Structure alignment based on coding of local geometric measures, BMC Bioinformatics 7:346, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 346
-
-
Chang, P.L.1
Rinne, A.W.2
Dewey, T.G.3
-
17
-
-
0019887799
-
Identification of common moleculax subsequences
-
Smith TF, Waterman MS, Identification of common moleculax subsequences, J Mol Biol 147(1):195-197, 1981.
-
(1981)
J Mol Biol
, vol.147
, Issue.1
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
18
-
-
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 48(3):443-453, 1970.
-
(1970)
J Mol Biol
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
19
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski R, MacArthur M, Moss D, Thornton J, PROCHECK: A program to check the stereochemical quality of protein structures, J Appl Cryst 26:283-291, 1993.
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.1
MacArthur, M.2
Moss, D.3
Thornton, J.4
-
21
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol Biol Evol 4 4):406-425, 1987.
-
(1987)
Mol Biol Evol
, vol.4
, Issue.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
22
-
-
0001336205
-
Phylogenetic inference
-
Hillis DM, Mortz C, Mable B eds, 2nd ed, Sinauer Associates, Sunderland, MA, pp
-
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM, Phylogenetic inference, in Hillis DM, Mortz C, Mable B (eds.), Molecular Systematics, 2nd ed., Sinauer Associates, Sunderland, MA, pp. 407-514, 1996.
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
23
-
-
0030801002
-
A new generation of protein database search programs
-
and PSI-BLAST
-
Altschul SF, Madden TL, Schaffer 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 25(17):3389-3402, 1997.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, 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
Gapped, B.L.A.S.T.8
-
24
-
-
0030310317
-
Assessing the performance of fold recognition methods by rpeans of a comprehensive benchmark
-
Fischer D, Elofsson A, Rice D, Eisenberg D, Assessing the performance of fold recognition methods by rpeans of a comprehensive benchmark, Pac Symp Biocomput, pp. 300-318, 1996.
-
(1996)
Pac Symp Biocomput
, pp. 300-318
-
-
Fischer, D.1
Elofsson, A.2
Rice, D.3
Eisenberg, D.4
-
25
-
-
0024066065
-
The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases
-
Bode W, Engh R, Musil D, Thiele U, Huber R, Karshikov A, Brzin J, Kos J, Turk V, The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases, EMBO J 7(8):2593-2599, 1988.
-
(1988)
EMBO J
, vol.7
, Issue.8
, pp. 2593-2599
-
-
Bode, W.1
Engh, R.2
Musil, D.3
Thiele, U.4
Huber, R.5
Karshikov, A.6
Brzin, J.7
Kos, J.8
Turk, V.9
-
26
-
-
0027527431
-
Two crystal structures of a potently sweet protein. Natural monellin at 2.75 Å resolution and single-chain monellin at 1.7 Å resolution
-
Somoza JR, Jiang F, Tong L, Kang CH, Cho JM, Kim SH, Two crystal structures of a potently sweet protein. Natural monellin at 2.75 Å resolution and single-chain monellin at 1.7 Å resolution, J Mol Biol 234(2):390-404, 1993.
-
(1993)
J Mol Biol
, vol.234
, Issue.2
, pp. 390-404
-
-
Somoza, J.R.1
Jiang, F.2
Tong, L.3
Kang, C.H.4
Cho, J.M.5
Kim, S.H.6
-
27
-
-
4143115703
-
Domain swapping in N-truncated human cystatin C
-
Janowski R, Abrahamson M, Grubb A, Jaskolski M, Domain swapping in N-truncated human cystatin C, J Mol Biol 341(1):151-160, 2004.
-
(2004)
J Mol Biol
, vol.341
, Issue.1
, pp. 151-160
-
-
Janowski, R.1
Abrahamson, M.2
Grubb, A.3
Jaskolski, M.4
-
28
-
-
0037452726
-
The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
-
Kamtekax S, Kennedy VVD, Wang J, Stathopoulos C, Soll D, Steitz TA, The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases, Proc Natl Acad Sci USA 100(4):1673-1678, 2003.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.4
, pp. 1673-1678
-
-
Kamtekax, S.1
Kennedy, V.V.D.2
Wang, J.3
Stathopoulos, C.4
Soll, D.5
Steitz, T.A.6
-
29
-
-
0033548581
-
Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine
-
Arnez JG, Dock-Bregeon AC, Moras D, Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine, J Mol Biol 286(5):1449-1459, 1999.
-
(1999)
J Mol Biol
, vol.286
, Issue.5
, pp. 1449-1459
-
-
Arnez, J.G.1
Dock-Bregeon, A.C.2
Moras, D.3
-
30
-
-
0346848759
-
On the evolution of structure in aminoacyl-tRNA synthetases
-
O'Donoghue P, Luthey-Schulten Z, On the evolution of structure in aminoacyl-tRNA synthetases, Microbiol Mol Biol Rev 67 4):550-573, 2003.
-
(2003)
Microbiol Mol Biol Rev
, vol.67
, Issue.4
, pp. 550-573
-
-
O'Donoghue, P.1
Luthey-Schulten, Z.2
-
31
-
-
16244404569
-
Molecular fragment replacement approach to protein structure determination by chemical shift and dipolax homology database mining
-
Kontaxis G, Delaglio F, Bax A, Molecular fragment replacement approach to protein structure determination by chemical shift and dipolax homology database mining, Methods Enzymol 394:42-78, 2005.
-
(2005)
Methods Enzymol
, vol.394
, pp. 42-78
-
-
Kontaxis, G.1
Delaglio, F.2
Bax, A.3
-
32
-
-
3242887695
-
Protein structure prediction and analysis using the Robetta server
-
Web Server issue:W526-W531
-
Kim DE, Chivian D, Baker D, Protein structure prediction and analysis using the Robetta server, Nucleic Acids Res 32(Web Server issue):W526-W531, 2004.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
-
33
-
-
0032104477
-
How far divergent evolution goes in proteins
-
Murzin AG, How far divergent evolution goes in proteins, Curr Opin Struct Biol 8(3):380-387, 1998.
-
(1998)
Curr Opin Struct Biol
, vol.8
, Issue.3
, pp. 380-387
-
-
Murzin, A.G.1
-
34
-
-
33644818869
-
Physical origins of protein superfamilies
-
Zeldovich KB, Berezovsky IN, Shakhnovich EI, Physical origins of protein superfamilies, J Mol Biol 357(4):1335-1343, 2006.
-
(2006)
J Mol Biol
, vol.357
, Issue.4
, pp. 1335-1343
-
-
Zeldovich, K.B.1
Berezovsky, I.N.2
Shakhnovich, E.I.3
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