-
1
-
-
0041620359
-
MATRAS: A program for protein 3D structure comparison
-
Kawabata, T. (2003) MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res., 31, 3367-3369.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3367-3369
-
-
Kawabata, T.1
-
2
-
-
48449084095
-
RAPIDO: A web server for the alignment of protein structures in the presence of conformational changes
-
Mosca, R. and Schneider, T.R. (2008) RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Res., 36, 42-46.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 42-46
-
-
Mosca, R.1
Schneider, T.R.2
-
3
-
-
67849090550
-
The SALAMI protein structure search server
-
Margraf, T., Schenk, G. and Torda, A.E. (2009) The SALAMI protein structure search server. Nucleic Acids Res., 37, 480-484.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 480-484
-
-
Margraf, T.1
Schenk, G.2
Torda, A.E.3
-
4
-
-
77954288774
-
Dali server: Conservation mapping in 3D
-
Holm, L. and Rosenström, P. (2010) Dali server: conservation mapping in 3d. Nucleic Acids Res., 38, 545-549.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 545-549
-
-
Holm, L.1
Rosenström, P.2
-
5
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
Hasegawa, H. and Holm, L. (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol., 19, 341-348.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
6
-
-
34548304928
-
Comparative analysis of protein structure alignments
-
Mayr, G., Domingues, F.S. and Lackner, P. (2007) Comparative analysis of protein structure alignments. BMC Struct Biol., 7, 50-50.
-
(2007)
BMC Struct Biol.
, vol.7
, pp. 50-50
-
-
Mayr, G.1
Domingues, F.S.2
Lackner, P.3
-
7
-
-
33745596822
-
Integrating multiattribute similarity networks for robust representation of the protein space
-
Camoglu, O., Can, T. and Singh, A.K. (2006) Integrating multiattribute similarity networks for robust representation of the protein space. Bioinformatics, 22, 1585-1592.
-
(2006)
Bioinformatics
, vol.22
, pp. 1585-1592
-
-
Camoglu, O.1
Can, T.2
Singh, A.K.3
-
8
-
-
38949177447
-
Procksi: A decision support system for protein (structure) comparison, knowledge, similarity and information
-
Barthel, D., Hirst, J.D., Blazewicz, J., Burke, E.K. and Krasnogor, N. (2007) ProCKSI: a decision support system for protein (structure) comparison, knowledge, similarity and information. BMC Bioinformatics, 8, 416-416.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 416-416
-
-
Barthel, D.1
Hirst, J.D.2
Blazewicz, J.3
Burke, E.K.4
Krasnogor, N.5
-
9
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
10
-
-
0028598811
-
Flexible algorithm for direct multiple alignment of protein structures and sequences
-
Godzik, A. and Skolnick, J. (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS, 10, 587-596.
-
(1994)
CABIOS
, vol.10
, pp. 587-596
-
-
Godzik, A.1
Skolnick, J.2
-
11
-
-
0034308164
-
Protein structure comparison using the markov transition model of evolution
-
Kawabata, T. and Nishikawa, K. (2000) Protein structure comparison using the Markov transition model of evolution. Proteins, 41, 108-122.
-
(2000)
Proteins
, vol.41
, pp. 108-122
-
-
Kawabata, T.1
Nishikawa, K.2
-
12
-
-
77956539084
-
Towards optimal alignment of protein structure distance matrices
-
Wohlers, I., Domingues, F.S. and Klau, G.W. (2010) Towards optimal alignment of protein structure distance matrices. Bioinformatics, 26, 2273-2280.
-
(2010)
Bioinformatics
, vol.26
, pp. 2273-2280
-
-
Wohlers, I.1
Domingues, F.S.2
Klau, G.W.3
-
13
-
-
78651321269
-
Maximum contact map overlap revisited
-
Andonov, R., Malod-Dognin, N. and Yanev, N. (2011) Maximum contact map overlap revisited. J. Comput. Biol., 18, 27-41.
-
(2011)
J. Comput. Biol.
, vol.18
, pp. 27-41
-
-
Andonov, R.1
Malod-Dognin, N.2
Yanev, N.3
-
14
-
-
79960116362
-
Algorithm engineering for optimal alignment of protein structure distance matrices
-
Wohlers, I., Andonov, R. and Klau, G.W. (2011) Algorithm engineering for optimal alignment of protein structure distance matrices. Optimization Lett., 5, 421-433.
-
(2011)
Optimization Lett.
, vol.5
, pp. 421-433
-
-
Wohlers, I.1
Andonov, R.2
Klau, G.W.3
-
16
-
-
0344033635
-
PDB file parser and structure class implemented in python
-
Hamelryck, T. and Manderick, B. (2003) PDB file parser and structure class implemented in python. Bioinformatics, 19, 2308-2310.
-
(2003)
Bioinformatics
, vol.19
, pp. 2308-2310
-
-
Hamelryck, T.1
Manderick, B.2
-
17
-
-
70349464982
-
Accuracy analysis of multiple structure alignments
-
Berbalk, C., Schwaiger, C.S. and Lackner, P. (2009) Accuracy analysis of multiple structure alignments. Protein Sci., 18, 2027-2035.
-
(2009)
Protein Sci.
, vol.18
, pp. 2027-2035
-
-
Berbalk, C.1
Schwaiger, C.S.2
Lackner, P.3
-
18
-
-
33846074754
-
SISYPHUS-structural alignments for proteins with non-trivial relationships
-
Andreeva, A., PrlićA., Hubbard, T.J. and Murzin, A.G. (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res., 35, 253-259.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 253-259
-
-
Andreeva, A.1
Prlić, A.2
Hubbard, T.J.3
Murzin, A.G.4
-
19
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic 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
-
20
-
-
27544448536
-
Implementing the ihop concept for navigation of biomedical literature
-
Hoffmann, R. and Valencia, A. (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics, 21(Suppl. 2), 252-258.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
, pp. 252-258
-
-
Hoffmann, R.1
Valencia, A.2
-
21
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
22
-
-
0345616428
-
A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain
-
Shih, S.C., Prag, G., Francis, S.A., Sutanto, M.A., Hurley, J.H. and Hicke, L. (2003) A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain. EMBO J., 22, 1273-1281.
-
(2003)
EMBO J.
, vol.22
, pp. 1273-1281
-
-
Shih, S.C.1
Prag, G.2
Francis, S.A.3
Sutanto, M.A.4
Hurley, J.H.5
Hicke, L.6
-
23
-
-
0032189646
-
Dictionary of recurrent domains in protein structures
-
Holm, L. and Sander, C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
-
(1998)
Proteins
, vol.33
, pp. 88-96
-
-
Holm, L.1
Sander, C.2
-
24
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
25
-
-
0034977013
-
A normalized root-mean-square distance for comparing protein three-dimensional structures
-
Carugo, O. and Pongor, S. (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci., 10, 1470-1473.
-
(2001)
Protein Sci.
, vol.10
, pp. 1470-1473
-
-
Carugo, O.1
Pongor, S.2
-
26
-
-
0029982530
-
The structural alignment between two proteins: Is there a unique answer?
-
Godzik, A. (1996) The structural alignment between two proteins: is there a unique answer? Protein Sci., 5, 1325-1338.
-
(1996)
Protein Sci.
, vol.5
, pp. 1325-1338
-
-
Godzik, A.1
-
27
-
-
17644392830
-
Tm-align: A protein structure alignment algorithm based on the tm-score
-
Zhang, Y. and Skolnick, J. (2005) Tm-align: a protein structure alignment algorithm based on the tm-score. Nucleic Acids Res, 33, 2302-2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
28
-
-
78650670093
-
Maximum cliques in protein structure comparison
-
Festa, P. (ed.) Springer
-
Malod-Dognin, N., Andonov, R. and Yanev, N. (2010) Maximum cliques in protein structure comparison. In: Festa, P. (ed.), SEA, Vol. 6049 of Lecture Notes in Computer Science. Springer, pp. 106-117.
-
(2010)
SEA 6049 of Lecture Notes in Computer Science
, pp. 106-117
-
-
Malod-Dognin, N.1
Andonov, R.2
Yanev, N.3
-
29
-
-
39749202824
-
Hingeprot: Automated prediction of hinges in protein structures
-
Emekli, U., Schneidman-Duhovny, D., Wolfson, H.J., Nussinov, R. and Haliloglu, T. (2008) Hingeprot: automated prediction of hinges in protein structures. Proteins, 70, 1219-1227.
-
(2008)
Proteins
, vol.70
, pp. 1219-1227
-
-
Emekli, U.1
Schneidman-Duhovny, D.2
Wolfson, H.J.3
Nussinov, R.4
Haliloglu, T.5
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