-
1
-
-
78651321269
-
Maximum contact map overlap revisited
-
R. Andonov, N. Malod-Dognin, and N. Yanev, "Maximum Contact Map Overlap Revisited," J. Computational Biology, vol. 18, no. 1, pp. 1-15, 2011.
-
(2011)
J. Computational Biology
, vol.18
, Issue.1
, pp. 1-15
-
-
Andonov, R.1
Malod-Dognin, N.2
Yanev, N.3
-
2
-
-
56649084996
-
An efficient lagrangian relaxation for the contact map overlap problem
-
R. Andonov, N. Yanev, and N. Malod-Dognin, "An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem," Proc. WABI '08: Eighth Int'l Workshop Algorithms in Bioinformatics, pp. 162-173, 2008.
-
(2008)
Proc. WABI '08: Eighth Int'l Workshop Algorithms in Bioinformatics
, pp. 162-173
-
-
Andonov, R.1
Yanev, N.2
Malod-Dognin, N.3
-
3
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
DOI 10.1093/nar/gkm993
-
A. Andreeva, D. Howorth, J.-M. Chandonia, S.E. Brenner, T.J.P. Hubbard, C. Chothia, and A.G. Murzin, "Data Growth and Its Impact on the Scop Database: New Developments," Nucleic Acids Research, vol. 36 (Database issue), pp. D419-D425, Jan. 2008. (Pubitemid 351149760)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.-M.3
Brenner, S.E.4
Hubbard, T.J.P.5
Chothia, C.6
Murzin, A.G.7
-
4
-
-
0033954256
-
The protein data bank
-
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne, "The Protein Data Bank," Nucleic Acids Research, vol. 28, no. 1, pp. 235-242, Jan. 2000. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, 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
-
5
-
-
0142091424
-
Matching protein structures with fuzzy alignments
-
DOI 10.1073/pnas.1635048100
-
R. Blankenbecler, M. Ohlsson, C. Peterson, and M. Ringner, "Matching Protein Structures with Fuzzy Alignments," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 21, pp. 11936-11940, Oct. 2003. (Pubitemid 37271493)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.21
, pp. 11936-11940
-
-
Blankenbecler, R.1
Ohlsson, M.2
Peterson, C.3
Ringner, M.4
-
7
-
-
1842451398
-
1001 Optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap
-
DOI 10.1089/106652704773416876
-
A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz, "1001 Optimal Pdb Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap," J. Computational Biology, vol. 11, no. 1, pp. 27-52, 2004. (Pubitemid 38429362)
-
(2004)
Journal of Computational Biology
, vol.11
, Issue.1
, pp. 27-52
-
-
Caprara, A.1
Carr, R.2
Istrail, S.3
Lancia, G.4
Walenz, B.5
-
8
-
-
0348129526
-
The ASTRAL compendium in 2004
-
J.-M. Chandonia, G. Hon, N.S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S.E. Brenner, "The Astral Compendium in 2004," Nucleic Acids Research, vol. 32 (Database issue), pp. D189-D192, Jan. 2004. (Pubitemid 38081635)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Chandonia, J.-M.1
Hon, G.2
Walker, N.S.3
Lo Conte, L.4
Koehl, P.5
Levitt, M.6
Brenner, S.E.7
-
9
-
-
33748955342
-
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison
-
article no. 18
-
L. Chen, L.-Y. Wu, Y. Wang, S. Zhang, and X.-S. Zhang, "Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison," BMC Structural Biology, vol. 6, article no. 18, 2006.
-
(2006)
BMC Structural Biology
, vol.6
-
-
Chen, L.1
Wu, L.-Y.2
Wang, Y.3
Zhang, S.4
Zhang, X.-S.5
-
10
-
-
65649092976
-
Biopython: Freely available python tools for computational molecular biology and bioinformatics
-
June
-
P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, and M.J.L. de Hoon, "Biopython: Freely Available Python Tools for Computational Molecular Biology and Bioinformatics," Bioinformatics, vol. 25, no. 11, pp. 1422-1423, June 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.11
, pp. 1422-1423
-
-
Cock, P.J.A.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
Dalke, A.6
Friedberg, I.7
Hamelryck, T.8
Kauff, F.9
Wilczynski, B.10
De Hoon, M.J.L.11
-
14
-
-
66549119395
-
Advances and pitfalls of protein structural alignment
-
June
-
H. Hasegawa and L. Holm, "Advances and Pitfalls of Protein Structural Alignment," Current Opinion in Structural Biology, vol. 19, no. 3, pp. 341-348, June 2009.
-
(2009)
Current Opinion in Structural Biology
, vol.19
, Issue.3
, pp. 341-348
-
-
Hasegawa, H.1
Holm, L.2
-
15
-
-
0021097083
-
The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem
-
Oct.
-
T.F. Havel, I.D. Kuntz, and G.M. Crippen, "The Combinatorial Distance Geometry Method for the Calculation of Molecular Conformation. i. a New Approach to an Old Problem," J. Theoretical Biology, vol. 104, no. 3, pp. 359-381, Oct. 1983.
-
(1983)
J. Theoretical Biology
, vol.104
, Issue.3
, pp. 359-381
-
-
Havel, T.F.1
Kuntz, I.D.2
Crippen, G.M.3
-
16
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
DOI 10.1006/jmbi.1993.1489
-
L. Holm and C. Sander, "Protein Structure Comparison by Alignment of Distance Matrices," J. Molecular Biology, vol. 233, no. 1, pp. 123-138, Sept. 1993. (Pubitemid 23288916)
-
(1993)
Journal of Molecular Biology
, vol.233
, Issue.1
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
18
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
W. Kabsch, "A Discussion of the Solution for the Best Rotation to Relate Two Sets of Vectors," Acta Crystallographica A, vol. 34, pp. 827-828, 1978.
-
(1978)
Acta Crystallographica A
, vol.34
, pp. 827-828
-
-
Kabsch, W.1
-
19
-
-
0034826884
-
Optimal pdb structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem
-
G. Lancia, R. Carr, B. Walenz, and S. Istrail, "101 Optimal Pdb Structure Alignments: A Branch-and-Cut Algorithm for the Maximum Contact Map Overlap Problem," Proc. Fifth Ann. Int'l Conf. Computational Biology, pp. 143-202, 2001.
-
(2001)
Proc. Fifth Ann. Int'l Conf. Computational Biology
, pp. 143-202
-
-
Lancia, G.1
Carr, R.2
Walenz, B.3
Istrail, S.4
-
20
-
-
77956526859
-
Fast overlapping of protein contact maps by alignment of eigenvectors
-
P. Di Lena, P. Fariselli, L. Margara, M. Vassura, and R. Casadio, "Fast Overlapping of Protein Contact Maps by Alignment of Eigenvectors," Bioinformatics, vol. 26, no. 18, pp. 2250-2258, 2010.
-
(2010)
Bioinformatics
, vol.26
, Issue.18
, pp. 2250-2258
-
-
Di Lena, P.1
Fariselli, P.2
Margara, L.3
Vassura, M.4
Casadio, R.5
-
21
-
-
38949150854
-
Matt: Local flexibility aids protein multiple structure alignment
-
Jan.
-
M. Menke, B. Berger, and L. Cowen, "Matt: Local Flexibility Aids Protein Multiple Structure Alignment," PLoS Computational Biology, vol. 4, no. 1, p. e10, Jan. 2008.
-
(2008)
PLoS Computational Biology
, vol.4
, Issue.1
-
-
Menke, M.1
Berger, B.2
Cowen, L.3
-
22
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Mar.
-
S.B. Needleman and C.D. Wunsch, "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins," J. Moleculer Biology, vol. 48, no. 3, pp. 443-453, Mar. 1970.
-
(1970)
J. Moleculer Biology
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
24
-
-
47349099919
-
Search strategies in structural bioinformatics
-
DOI 10.2174/138920308784534032
-
M.T. Oakley, D. Barthel, Y. Bykov, J.M. Garibaldi, E.K. Burke, N. Krasnogor, and J.D. Hirst, "Search Strategies in Structural Bioinformatics," Current Protein and Peptide Science, vol. 9, no. 3, pp. 260-274, June 2008. (Pubitemid 351997842)
-
(2008)
Current Protein and Peptide Science
, vol.9
, Issue.3
, pp. 260-274
-
-
Oakley, M.T.1
Barthel, D.2
Bykov, Y.3
Garibaldi, J.M.4
Burke, E.K.5
Krasnogor, N.6
Hirst, J.D.7
-
25
-
-
70350682039
-
Algorithms for optimal protein structure alignment
-
Nov.
-
A. Poleksic, "Algorithms for Optimal Protein Structure Alignment," Bioinformatics, vol. 25, no. 21, pp. 2751-2756, Nov. 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.21
, pp. 2751-2756
-
-
Poleksic, A.1
-
26
-
-
0027409570
-
A geometrical constraint approach for reproducing the native backbone conformation of a protein
-
DOI 10.1002/prot.340150209
-
S. Saitoh, T. Nakai, and K. Nishikawa, "A Geometrical Constraint Approach for Reproducing the Native Backbone Conformation of a Protein," Proteins, vol. 15, no. 2, pp. 191-204, Feb. 1993. (Pubitemid 23060597)
-
(1993)
Proteins: Structure, Function and Genetics
, vol.15
, Issue.2
, pp. 191-204
-
-
Saitoh, S.1
Nakai, T.2
Nishikawa, K.3
-
27
-
-
77953742473
-
Fast protein structure alignment
-
M. Borodovsky, ed., Springer-Verlag
-
Y. Shibberu, A. Holder, and K. Lutz, "Fast Protein Structure Alignment," Lecture Notes in Computer Science, M. Borodovsky, ed., vol. 6053, pp. 152-165, Springer-Verlag, 2010.
-
(2010)
Lecture Notes in Computer Science
, vol.6053
, pp. 152-165
-
-
Shibberu, Y.1
Holder, A.2
Lutz, K.3
-
28
-
-
77952237288
-
Fast hinge detection algorithms for flexible protein structures
-
Apr.-June
-
T. Shibuya, "Fast Hinge Detection Algorithms for Flexible Protein Structures," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 333-341, Apr.-June 2010.
-
(2010)
IEEE/ACM Trans. Computational Biology and Bioinformatics
, vol.7
, Issue.2
, pp. 333-341
-
-
Shibuya, T.1
-
29
-
-
77649155262
-
Linear-Time protein 3D structure searching with insertions and deletions
-
article no. 7
-
T. Shibuya, J. Jansson, and K. Sadakane, "Linear-Time Protein 3D Structure Searching with Insertions and Deletions," Algorithms for Molecular Biology, vol. 5, article no. 7, 2010.
-
(2010)
Algorithms for Molecular Biology
, vol.5
-
-
Shibuya, T.1
Jansson, J.2
Sadakane, K.3
-
30
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
I.N. Shindyalov and P.E. Bourne, "Protein Structure Alignment by Incremental Combinatorial Extension (ce) of the Optimal Path," Protein Eng., vol. 11, no. 9, pp. 739-747, Sept. 1998. (Pubitemid 28434482)
-
(1998)
Protein Engineering
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
31
-
-
0030627407
-
Recovery of protein structure from contact maps
-
M. Vendruscolo, E. Kussell, and E. Domany, "Recovery of Protein Structure from Contact Maps," Folding and Design, vol. 2, no. 5, pp. 295-306, 1997. (Pubitemid 127740552)
-
(1997)
Folding and Design
, vol.2
, Issue.5
, pp. 295-306
-
-
Vendruscolo, M.1
Kussell, E.2
Domany, E.3
-
32
-
-
75449084362
-
Evaluating protein similarity from coarse structures
-
Oct.-Dec.
-
Y. Wang, L.-Y. Wu, J.-H. Zhang, Z.-W. Zhan, X.-S. Zhang, and L. Chen, "Evaluating Protein Similarity from Coarse Structures," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 583-593, Oct.-Dec. 2009.
-
(2009)
IEEE/ ACM Trans. Computational Biology and Bioinformatics
, vol.6
, Issue.4
, pp. 583-593
-
-
Wang, Y.1
Wu, L.-Y.2
Zhang, J.-H.3
Zhan, Z.-W.4
Zhang, X.-S.5
Chen, L.6
-
33
-
-
34447288497
-
A reduction-based exact algorithm for the contact map overlap problem
-
DOI 10.1089/cmb.2007.R007
-
W. Xie and N.V. Sahinidis, "A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem," J. Computational Biology, vol. 14, no. 5, pp. 637-654, June 2007. (Pubitemid 47047818)
-
(2007)
Journal of Computational Biology
, vol.14
, Issue.5
, pp. 637-654
-
-
Xie, W.1
Sahinidis, N.V.2
|