-
1
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
-
10.1016/j.jmb.2004.12.032, 2692023, 15701525
-
Kolodny R, Koehl P, Levitt M. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol 2005, 346(4):1173-88. 10.1016/j.jmb.2004.12.032, 2692023, 15701525.
-
(2005)
J Mol Biol
, vol.346
, Issue.4
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
2
-
-
0030979555
-
Circular permutations of natural protein sequences: structural evidence
-
10.1016/S0959-440X(97)80061-9, 9204286
-
Lindqvist Y, Schneider G. Circular permutations of natural protein sequences: structural evidence. Curr Opin Struct Biol 1997, 7(3):422-7. 10.1016/S0959-440X(97)80061-9, 9204286.
-
(1997)
Curr Opin Struct Biol
, vol.7
, Issue.3
, pp. 422-427
-
-
Lindqvist, Y.1
Schneider, G.2
-
3
-
-
0035783063
-
Fold change in evolution of protein structures
-
10.1006/jsbi.2001.4335, 11551177
-
Grishin NV. Fold change in evolution of protein structures. J Struct Biol 2001, 134(2-3):167-85. 10.1006/jsbi.2001.4335, 11551177.
-
(2001)
J Struct Biol
, vol.134
, Issue.2-3
, pp. 167-185
-
-
Grishin, N.V.1
-
4
-
-
3142745171
-
Alternative alignments from comparison of protein structures
-
10.1002/prot.20124, 15229884
-
Shih ES, Hwang MJ. Alternative alignments from comparison of protein structures. Proteins 2004, 56(3):519-27. 10.1002/prot.20124, 15229884.
-
(2004)
Proteins
, vol.56
, Issue.3
, pp. 519-527
-
-
Shih, E.S.1
Hwang, M.J.2
-
5
-
-
38649086688
-
A comprehensive analysis of non-sequential alignments between all protein structures
-
10.1186/1472-6807-7-78, 2213659, 18005453
-
Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Struct Biol 2007, 7:78. 10.1186/1472-6807-7-78, 2213659, 18005453.
-
(2007)
BMC Struct Biol
, vol.7
, pp. 78
-
-
Abyzov, A.1
Ilyin, V.A.2
-
6
-
-
33846074754
-
SISYPHUS-structural alignments for proteins with non-trivial relationships
-
1635320, 17068077
-
Andreeva A, Prlic A, Hubbard TJ, Murzin AG. SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res 2007, 35(Database issue):D253-9. 1635320, 17068077.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.DATABASE ISSUE
-
-
Andreeva, A.1
Prlic, A.2
Hubbard, T.J.3
Murzin, A.G.4
-
7
-
-
34548304928
-
Comparative analysis of protein structure alignments
-
10.1186/1472-6807-7-50, 1959231, 17672887
-
Mayr G, Domingues FS, Lackner P. Comparative analysis of protein structure alignments. BMC Struct Biol 2007, 7:50. 10.1186/1472-6807-7-50, 1959231, 17672887.
-
(2007)
BMC Struct Biol
, vol.7
, pp. 50
-
-
Mayr, G.1
Domingues, F.S.2
Lackner, P.3
-
8
-
-
0029948001
-
SSAP: sequential structure alignment program for protein structure comparison
-
Orengo CA, Taylor WR. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol 1996, 266:617-35.
-
(1996)
Methods Enzymol
, vol.266
, pp. 617-635
-
-
Orengo, C.A.1
Taylor, W.R.2
-
9
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
10.1006/jmbi.1993.1489, 8377180
-
Holm L, Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-38. 10.1006/jmbi.1993.1489, 8377180.
-
(1993)
J Mol Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
10
-
-
77956539084
-
Towards optimal alignment of protein structure distance matrices
-
10.1093/bioinformatics/btq420, 20639543
-
Wohlers I, Domingues FS, Klau GW. Towards optimal alignment of protein structure distance matrices. Bioinformatics 2010, 26(18):2273-80. 10.1093/bioinformatics/btq420, 20639543.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
, pp. 2273-2280
-
-
Wohlers, I.1
Domingues, F.S.2
Klau, G.W.3
-
11
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
10.1093/protein/11.9.739, 9796821
-
Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11(9):739-47. 10.1093/protein/11.9.739, 9796821.
-
(1998)
Protein Eng
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
12
-
-
0028838717
-
Threading a database of protein cores
-
10.1002/prot.340230309, 8710828
-
Madej T, Gibrat JF, Bryant SH. Threading a database of protein cores. Proteins 1995, 23(3):356-69. 10.1002/prot.340230309, 8710828.
-
(1995)
Proteins
, vol.23
, Issue.3
, pp. 356-369
-
-
Madej, T.1
Gibrat, J.F.2
Bryant, S.H.3
-
13
-
-
0029796428
-
SARFing the PDB
-
10.1093/protein/9.9.727, 8888137
-
Alexandrov N. SARFing the PDB. Protein Engineering 1996, 9(9):727. 10.1093/protein/9.9.727, 8888137.
-
(1996)
Protein Engineering
, vol.9
, Issue.9
, pp. 727
-
-
Alexandrov, N.1
-
14
-
-
0034308164
-
Protein structure comparison using the markov transition model of evolution
-
10.1002/1097-0134(20001001)41:1<108::AID-PROT130>3.0.CO;2-S, 10944398
-
Kawabata T, Nishikawa K. Protein structure comparison using the markov transition model of evolution. Proteins 2000, 41:108-22. 10.1002/1097-0134(20001001)41:1<108::AID-PROT130>3.0.CO;2-S, 10944398.
-
(2000)
Proteins
, vol.41
, pp. 108-122
-
-
Kawabata, T.1
Nishikawa, K.2
-
15
-
-
48249130416
-
Novel protein folds and their nonsequential structural analogs
-
10.1110/ps.035469.108, 2492825, 18583523
-
Guerler A, Knapp EW. Novel protein folds and their nonsequential structural analogs. Protein Sci 2008, 17(8):1374-82. 10.1110/ps.035469.108, 2492825, 18583523.
-
(2008)
Protein Sci
, vol.17
, Issue.8
, pp. 1374-1382
-
-
Guerler, A.1
Knapp, E.W.2
-
16
-
-
0027238108
-
A computer vision based technique for 3-D sequence-independent structural comparison of proteins
-
10.1093/protein/6.3.279, 8506262
-
Bachar O, Fischer D, Nussinov R, Wolfson H. A computer vision based technique for 3-D sequence-independent structural comparison of proteins. Protein Eng 1993, 6(3):279-88. 10.1093/protein/6.3.279, 8506262.
-
(1993)
Protein Eng
, vol.6
, Issue.3
, pp. 279-288
-
-
Bachar, O.1
Fischer, D.2
Nussinov, R.3
Wolfson, H.4
-
17
-
-
0031697713
-
A geometric algorithm to find small but highly similar 3D substructures in proteins
-
10.1093/bioinformatics/14.6.516, 9694990
-
Pennec X, Ayache N. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 1998, 14(6):516-22. 10.1093/bioinformatics/14.6.516, 9694990.
-
(1998)
Bioinformatics
, vol.14
, Issue.6
, pp. 516-522
-
-
Pennec, X.1
Ayache, N.2
-
18
-
-
55649116694
-
Comparison of protein structures by growing neighborhood alignments
-
10.1186/1471-2105-8-77, 1828169, 17338826
-
Bhattacharya S, Bhattacharyya C, Chandra NR. Comparison of protein structures by growing neighborhood alignments. BMC Bioinformatics 2007, 8:77. 10.1186/1471-2105-8-77, 1828169, 17338826.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 77
-
-
Bhattacharya, S.1
Bhattacharyya, C.2
Chandra, N.R.3
-
19
-
-
0033833116
-
Protein structure alignment using environmental profiles
-
10.1093/protein/13.8.535, 10964982
-
Jung J, Lee B. Protein structure alignment using environmental profiles. Protein Eng 2000, 13(8):535-43. 10.1093/protein/13.8.535, 10964982.
-
(2000)
Protein Eng
, vol.13
, Issue.8
, pp. 535-543
-
-
Jung, J.1
Lee, B.2
-
20
-
-
3042533397
-
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
-
10.1110/ps.04672604, 2279929, 15215530
-
Ilyin VA, Abyzov A, Leslin CM. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci 2004, 13(7):1865-74. 10.1110/ps.04672604, 2279929, 15215530.
-
(2004)
Protein Sci
, vol.13
, Issue.7
, pp. 1865-1874
-
-
Ilyin, V.A.1
Abyzov, A.2
Leslin, C.M.3
-
21
-
-
79960775974
-
3d-blast: 3d protein structure alignment, comparison, and classification using spherical polar fourier correlations
-
Mavridis L, Ritchie DW. 3d-blast: 3d protein structure alignment, comparison, and classification using spherical polar fourier correlations. Pac Symp Biocomput 2010, 281-92.
-
(2010)
Pac Symp Biocomput
, pp. 281-292
-
-
Mavridis, L.1
Ritchie, D.W.2
-
22
-
-
3042581007
-
Flexible structure alignment by chaining aligned fragment pairs allowing twists
-
10.1093/bioinformatics/btg1086, 14534198
-
Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, 19(Suppl 2):ii246-55. 10.1093/bioinformatics/btg1086, 14534198.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Ye, Y.1
Godzik, A.2
-
23
-
-
1842450688
-
FlexProt: alignment of flexible protein structures without a predefinition of hinge regions
-
10.1089/106652704773416902, 15072690
-
Shatsky M, Nussinov R, Wolfson HJ. FlexProt: alignment of flexible protein structures without a predefinition of hinge regions. J Comput Biol 2004, 11:83-106. 10.1089/106652704773416902, 15072690.
-
(2004)
J Comput Biol
, vol.11
, pp. 83-106
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.J.3
-
24
-
-
67649221642
-
Flexible structural protein alignment by a sequence of local transformations
-
10.1093/bioinformatics/btp296, 2940242, 19417057
-
Rocha J, Segura J, Wilson RC, Dasgupta S. Flexible structural protein alignment by a sequence of local transformations. Bioinformatics 2009, 25(13):1625-31. 10.1093/bioinformatics/btp296, 2940242, 19417057.
-
(2009)
Bioinformatics
, vol.25
, Issue.13
, pp. 1625-1631
-
-
Rocha, J.1
Segura, J.2
Wilson, R.C.3
Dasgupta, S.4
-
25
-
-
77951197269
-
FlexSnap: Flexible Non-sequential Protein Structure Alignment
-
10.1186/1748-7188-5-12, 2846951, 20047669
-
Salem S, Zaki M, Bystroff C. FlexSnap: Flexible Non-sequential Protein Structure Alignment. Algorithms for Molecular Biology 2010, 5:12. 10.1186/1748-7188-5-12, 2846951, 20047669.
-
(2010)
Algorithms for Molecular Biology
, vol.5
, pp. 12
-
-
Salem, S.1
Zaki, M.2
Bystroff, C.3
-
26
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
10.1016/j.sbi.2009.04.003, 19481444
-
Hasegawa H, Holm L. Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 2009, 19(3):341-8. 10.1016/j.sbi.2009.04.003, 19481444.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.3
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
27
-
-
24744437347
-
A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins
-
10.1093/bioinformatics/btg1064, 14534176
-
Hvidsten TR, Kryshtafovych A, Komorowski J, Fidelis K. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins. Bioinformatics 2003, 19(Suppl 2):ii81-91. 10.1093/bioinformatics/btg1064, 14534176.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Hvidsten, T.R.1
Kryshtafovych, A.2
Komorowski, J.3
Fidelis, K.4
-
28
-
-
66149182894
-
Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions
-
10.1002/prot.22296, 19025980
-
Hvidsten TR, Kryshtafovych A, Fidelis K. Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Proteins 2009, 75(4):870-84. 10.1002/prot.22296, 19025980.
-
(2009)
Proteins
, vol.75
, Issue.4
, pp. 870-884
-
-
Hvidsten, T.R.1
Kryshtafovych, A.2
Fidelis, K.3
-
29
-
-
30344479439
-
CASP6 data processing and automatic evaluation at the protein structure prediction center
-
Kryshtafovych A, Milostan M, Szajkowski L, Daniluk P, Fidelis K. CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins 2005, 61(Suppl 7):19-23.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 19-23
-
-
Kryshtafovych, A.1
Milostan, M.2
Szajkowski, L.3
Daniluk, P.4
Fidelis, K.5
-
30
-
-
36749028144
-
New tools and expanded data analysis capabilities at the Protein Structure Prediction Center
-
2656758,2656758, 17705273
-
Kryshtafovych A, Prlic A, Dmytriv Z, Daniluk P, Milostan M, Eyrich V, Hubbard T, Fidelis K. New tools and expanded data analysis capabilities at the Protein Structure Prediction Center. Proteins 2007, 69(Suppl 8):19-26. 2656758,2656758, 17705273.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 19-26
-
-
Kryshtafovych, A.1
Prlic, A.2
Dmytriv, Z.3
Daniluk, P.4
Milostan, M.5
Eyrich, V.6
Hubbard, T.7
Fidelis, K.8
-
31
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 1976, 32(5):922-923.
-
(1976)
Acta Crystallographica Section A
, vol.32
, Issue.5
, pp. 922-923
-
-
Kabsch, W.1
-
32
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A 1978, 34(5):827-828.
-
(1978)
Acta Crystallographica Section A
, vol.34
, Issue.5
, pp. 827-828
-
-
Kabsch, W.1
-
33
-
-
0030777303
-
CATH-a hierarchic classification of protein domain structures
-
10.1016/S0969-2126(97)00260-8, 9309224
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-108. 10.1016/S0969-2126(97)00260-8, 9309224.
-
(1997)
Structure
, vol.5
, Issue.8
, 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
-
34
-
-
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(4):536-40.
-
(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
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
10.1093/nar/gkg571, 168977, 12824330
-
Zemla A. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 2003, 31(13):3370-4. 10.1093/nar/gkg571, 168977, 12824330.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3370-3374
-
-
Zemla, A.1
-
36
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
10.1093/bioinformatics/16.6.566, 10980157
-
Holm L, Park J. DaliLite workbench for protein structure comparison. Bioinformatics 2000, 16(6):566-7. 10.1093/bioinformatics/16.6.566, 10980157.
-
(2000)
Bioinformatics
, vol.16
, Issue.6
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
37
-
-
0029000740
-
Swaposins: circular permutations within genes encoding saposin homologues
-
10.1016/S0968-0004(00)89003-9, 7610480
-
Ponting CP, Russell RB. Swaposins: circular permutations within genes encoding saposin homologues. Trends Biochem Sci 1995, 20(5):179-80. 10.1016/S0968-0004(00)89003-9, 7610480.
-
(1995)
Trends Biochem Sci
, vol.20
, Issue.5
, pp. 179-180
-
-
Ponting, C.P.1
Russell, R.B.2
-
38
-
-
0031253938
-
Saposin fold revealed by the NMR structure of NK-lysin
-
10.1038/nsb1097-793, 9334742
-
Liepinsh E, Andersson M, Ruysschaert JM, Otting G. Saposin fold revealed by the NMR structure of NK-lysin. Nat Struct Biol 1997, 4(10):793-5. 10.1038/nsb1097-793, 9334742.
-
(1997)
Nat Struct Biol
, vol.4
, Issue.10
, pp. 793-795
-
-
Liepinsh, E.1
Andersson, M.2
Ruysschaert, J.M.3
Otting, G.4
-
39
-
-
0033565640
-
Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting
-
10.1093/emboj/18.14.3947, 1171470, 10406799
-
Kervinen J, Tobin GJ, Costa J, Waugh DS, Wlodawer A, Zdanov A. Crystal structure of plant aspartic proteinase prophytepsin: inactivation and vacuolar targeting. EMBO J 1999, 18(14):3947-55. 10.1093/emboj/18.14.3947, 1171470, 10406799.
-
(1999)
EMBO J
, vol.18
, Issue.14
, pp. 3947-3955
-
-
Kervinen, J.1
Tobin, G.J.2
Costa, J.3
Waugh, D.S.4
Wlodawer, A.5
Zdanov, A.6
-
40
-
-
0035503309
-
Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms
-
10.1093/emboj/20.21.5813, 125706, 11689422
-
Niemann HH, Knetsch ML, Scherer A, Manstein DJ, Kull FJ. Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms. EMBO J 2001, 20(21):5813-21. 10.1093/emboj/20.21.5813, 125706, 11689422.
-
(2001)
EMBO J
, vol.20
, Issue.21
, pp. 5813-5821
-
-
Niemann, H.H.1
Knetsch, M.L.2
Scherer, A.3
Manstein, D.J.4
Kull, F.J.5
-
41
-
-
4444285829
-
Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain
-
10.1073/pnas.0405202101, 516547, 15331784
-
Shin DH, Lou Y, Jancarik J, Yokota H, Kim R, Kim SH. Crystal structure of YjeQ from Thermotoga maritima contains a circularly permuted GTPase domain. Proc Natl Acad Sci USA 2004, 101(36):13198-203. 10.1073/pnas.0405202101, 516547, 15331784.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.36
, pp. 13198-13203
-
-
Shin, D.H.1
Lou, Y.2
Jancarik, J.3
Yokota, H.4
Kim, R.5
Kim, S.H.6
-
42
-
-
33744528396
-
Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding
-
10.1093/nar/gkl178, 1450330, 16648363
-
Anand B, Verma SK, Prakash B. Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding. Nucleic Acids Res 2006, 34(8):2196-205. 10.1093/nar/gkl178, 1450330, 16648363.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.8
, pp. 2196-2205
-
-
Anand, B.1
Verma, S.K.2
Prakash, B.3
-
43
-
-
0031848334
-
Solution structure of cyanovirin-N, a potent HIV-inactivating protein
-
10.1038/828, 9665171
-
Bewley CA, Gustafson KR, Boyd MR, Covell DG, Bax A, Clore GM, Gronenborn AM. Solution structure of cyanovirin-N, a potent HIV-inactivating protein. Nat Struct Biol 1998, 5(7):571-8. 10.1038/828, 9665171.
-
(1998)
Nat Struct Biol
, vol.5
, Issue.7
, pp. 571-578
-
-
Bewley, C.A.1
Gustafson, K.R.2
Boyd, M.R.3
Covell, D.G.4
Bax, A.5
Clore, G.M.6
Gronenborn, A.M.7
-
44
-
-
0033532212
-
Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping
-
10.1006/jmbi.1999.2693, 10329150
-
Yang F, Bewley CA, Louis JM, Gustafson KR, Boyd MR, Gronenborn AM, Clore GM, Wlodawer A. Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping. J Mol Biol 1999, 288(3):403-12. 10.1006/jmbi.1999.2693, 10329150.
-
(1999)
J Mol Biol
, vol.288
, Issue.3
, pp. 403-412
-
-
Yang, F.1
Bewley, C.A.2
Louis, J.M.3
Gustafson, K.R.4
Boyd, M.R.5
Gronenborn, A.M.6
Clore, G.M.7
Wlodawer, A.8
-
45
-
-
0036113691
-
The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures
-
10.1016/S0969-2126(02)00758-X, 12015150
-
Barrientos LG, Louis JM, Botos I, Mori T, Han Z, O'Keefe BR, Boyd MR, Wlodawer A, Gronenborn AM. The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures. Structure 2002, 10(5):673-86. 10.1016/S0969-2126(02)00758-X, 12015150.
-
(2002)
Structure
, vol.10
, Issue.5
, pp. 673-686
-
-
Barrientos, L.G.1
Louis, J.M.2
Botos, I.3
Mori, T.4
Han, Z.5
O'Keefe, B.R.6
Boyd, M.R.7
Wlodawer, A.8
Gronenborn, A.M.9
-
46
-
-
13444262384
-
CDD: a Conserved Domain Database for protein classification
-
540023, 15608175
-
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res 2005, 33(Database issue):D192-6. 540023, 15608175.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.DATABASE ISSUE
-
-
Marchler-Bauer, A.1
Anderson, J.B.2
Cherukuri, P.F.3
DeWeese-Scott, C.4
Geer, L.Y.5
Gwadz, M.6
He, S.7
Hurwitz, D.I.8
Jackson, J.D.9
Ke, Z.10
Lanczycki, C.J.11
Liebert, C.A.12
Liu, C.13
Lu, F.14
Marchler, G.H.15
Mullokandov, M.16
Shoemaker, B.A.17
Simonyan, V.18
Song, J.S.19
Thiessen, P.A.20
Yamashita, R.A.21
Yin, J.J.22
Zhang, D.23
Bryant, S.H.24
more..
-
47
-
-
35448992938
-
Accuracy of structure-based sequence alignment of automatic methods
-
10.1186/1471-2105-8-355, 2039753, 17883866
-
Kim C, Lee B. Accuracy of structure-based sequence alignment of automatic methods. BMC Bioinformatics 2007, 8:355. 10.1186/1471-2105-8-355, 2039753, 17883866.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 355
-
-
Kim, C.1
Lee, B.2
-
48
-
-
59949099105
-
The meaning of alignment: lessons from structural diversity
-
10.1186/1471-2105-9-556, 2630330, 19105835
-
Pirovano W, Feenstra KA, Heringa J. The meaning of alignment: lessons from structural diversity. BMC Bioinformatics 2008, 9:556. 10.1186/1471-2105-9-556, 2630330, 19105835.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 556
-
-
Pirovano, W.1
Feenstra, K.A.2
Heringa, J.3
-
49
-
-
50949122245
-
Bridging protein local structures and protein functions
-
10.1007/s00726-008-0088-8, 18421562
-
Liu ZP, Wu LY, Wang Y, Zhang XS, Chen L. Bridging protein local structures and protein functions. Amino Acids 2008, 35(3):627-50. 10.1007/s00726-008-0088-8, 18421562.
-
(2008)
Amino Acids
, vol.35
, Issue.3
, pp. 627-650
-
-
Liu, Z.P.1
Wu, L.Y.2
Wang, Y.3
Zhang, X.S.4
Chen, L.5
-
50
-
-
44949122425
-
Exploring the structure and function paradigm
-
10.1016/j.sbi.2008.05.007, 2561214, 18554899
-
Redfern OC, Dessailly B, Orengo CA. Exploring the structure and function paradigm. Curr Opin Struct Biol 2008, 18(3):394-402. 10.1016/j.sbi.2008.05.007, 2561214, 18554899.
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.3
, pp. 394-402
-
-
Redfern, O.C.1
Dessailly, B.2
Orengo, C.A.3
-
51
-
-
41149134509
-
Sequence-similar, structure-dissimilar protein pairs in the PDB
-
10.1002/prot.21770, 2673347, 18004789
-
Kosloff M, Kolodny R. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 2008, 71(2):891-902. 10.1002/prot.21770, 2673347, 18004789.
-
(2008)
Proteins
, vol.71
, Issue.2
, pp. 891-902
-
-
Kosloff, M.1
Kolodny, R.2
-
52
-
-
65549127269
-
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts
-
10.1093/bioinformatics/btp149, 2677742, 19289446
-
Björkholm P, Daniluk P, Kryshtafovych A, Fidelis K, Andersson R, Hvidsten TR. Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics 2009, 25(10):1264-70. 10.1093/bioinformatics/btp149, 2677742, 19289446.
-
(2009)
Bioinformatics
, vol.25
, Issue.10
, pp. 1264-1270
-
-
Björkholm, P.1
Daniluk, P.2
Kryshtafovych, A.3
Fidelis, K.4
Andersson, R.5
Hvidsten, T.R.6
-
53
-
-
35448944862
-
Library of local descriptors models the core of proteins accurately
-
10.1002/prot.21393, 17623841
-
Drabikowski M, Nowakowski S, Tiuryn J. Library of local descriptors models the core of proteins accurately. Proteins 2007, 69(3):499-510. 10.1002/prot.21393, 17623841.
-
(2007)
Proteins
, vol.69
, Issue.3
, pp. 499-510
-
-
Drabikowski, M.1
Nowakowski, S.2
Tiuryn, J.3
-
54
-
-
33750049960
-
Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures
-
10.1002/prot.21163, 16948162
-
Strömbergsson H, Kryshtafovych A, Prusis P, Fidelis K, Wikberg JE, Komorowski J, Hvidsten TR. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Proteins 2006, 65(3):568-79. 10.1002/prot.21163, 16948162.
-
(2006)
Proteins
, vol.65
, Issue.3
, pp. 568-579
-
-
Strömbergsson, H.1
Kryshtafovych, A.2
Prusis, P.3
Fidelis, K.4
Wikberg, J.E.5
Komorowski, J.6
Hvidsten, T.R.7
-
55
-
-
57549114279
-
Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space
-
10.1021/ci800200e, 18937438
-
Strömbergsson H, Daniluk P, Kryshtafovych A, Fidelis K, Wikberg JE, Kleywegt GJ, Hvidsten TR. Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space. J Chem Inf Model 2008, 48(11):2278-88. 10.1021/ci800200e, 18937438.
-
(2008)
J Chem Inf Model
, vol.48
, Issue.11
, pp. 2278-2288
-
-
Strömbergsson, H.1
Daniluk, P.2
Kryshtafovych, A.3
Fidelis, K.4
Wikberg, J.E.5
Kleywegt, G.J.6
Hvidsten, T.R.7
-
57
-
-
5744249209
-
Equation of State Calculations by Fast Computing Machines
-
Metropolis N, Rosenbluth A, Rosenbluth M, Teller A, Teller E. Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics 1953, 21(6):1087.
-
(1953)
The Journal of Chemical Physics
, vol.21
, Issue.6
, pp. 1087
-
-
Metropolis, N.1
Rosenbluth, A.2
Rosenbluth, M.3
Teller, A.4
Teller, E.5
-
58
-
-
35949020425
-
Replica Monte Carlo simulation of spin glasses
-
10.1103/PhysRevLett.57.2607, 10033814
-
Swendsen RH, Wang JS. Replica Monte Carlo simulation of spin glasses. Phys Rev Lett 1986, 57(21):2607-2609. 10.1103/PhysRevLett.57.2607, 10033814.
-
(1986)
Phys Rev Lett
, vol.57
, Issue.21
, pp. 2607-2609
-
-
Swendsen, R.H.1
Wang, J.S.2
|