-
1
-
-
56649084996
-
An efficient Lagrangian relaxation for the contact map overlap problem
-
5251 of Lecture Notes in Computer Science. Springer, Berlin/Heidelberg
-
Andonov,R. et al. (2008) An efficient Lagrangian relaxation for the contact map overlap problem. In Proceedings of the 8th international workshop on Algorithms in Bioinformatics. Vol. 5251 of Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 162-173.
-
(2008)
Proceedings of the 8th international workshop on Algorithms in Bioinformatics
, pp. 162-173
-
-
Andonov, R.1
-
2
-
-
33846074754
-
SISYPHUS-structural alignments for proteins with nontrivial relationships
-
(Database issue)
-
Andreeva,A. et al. (2007) SISYPHUS-structural alignments for proteins with nontrivial relationships. Nucleic Acids Res., 35(Database issue), 253-259.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 253-259
-
-
Andreeva, A.1
-
3
-
-
0027238108
-
A computer vision based technique for 3-D sequenceindependent structural comparison of proteins
-
Bachar,O. et al. (1993) A computer vision based technique for 3-D sequenceindependent structural comparison of proteins. Protein Eng., 6, 279-288.
-
(1993)
Protein Eng.
, vol.6
, pp. 279-288
-
-
Bachar, O.1
-
4
-
-
34548348538
-
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
-
Bauer,M. et al. (2007)Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8, 271.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 271
-
-
Bauer, M.1
-
5
-
-
70349464982
-
Accuracy analysis of multiple structure alignments
-
Berbalk,C. et al. (2009) Accuracy analysis of multiple structure alignments. Protein Sci., 18, 2027-2035.
-
(2009)
Protein Sci.
, vol.18
, pp. 2027-2035
-
-
Berbalk, C.1
-
6
-
-
33846704538
-
Vorolign-fast structural alignment using Voronoi contacts
-
Birzele,F. et al. (2007) Vorolign-fast structural alignment using Voronoi contacts. Bioinformatics, 23, 205-211.
-
(2007)
Bioinformatics
, vol.23
, pp. 205-211
-
-
Birzele, F.1
-
7
-
-
1842451398
-
1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap
-
Caprara,A. et al. (2004) 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. J. Comput. Biol., 11, 27-52.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 27-52
-
-
Caprara, A.1
-
8
-
-
49549085536
-
Protein structure alignment considering phenotypic plasticity
-
Csaba,G. et al. (2008) Protein structure alignment considering phenotypic plasticity. Bioinformatics, 24, 98-104.
-
(2008)
Bioinformatics
, vol.24
, pp. 98-104
-
-
Csaba, G.1
-
9
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
Gotoh,O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
-
(1982)
J. Mol. Biol.
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
10
-
-
0029787639
-
A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution
-
Hara,T. et al. (1996) A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution. Biochemistry, 35, 11967-11974.
-
(1996)
Biochemistry
, vol.35
, pp. 11967-11974
-
-
Hara, T.1
-
11
-
-
49049123546
-
The theory and practice of distance geometry
-
Havel,T. et al. (1983) The theory and practice of distance geometry. Bull. Math. Biol., 45, 665-720.
-
(1983)
Bull. Math. Biol.
, vol.45
, pp. 665-720
-
-
Havel, T.1
-
12
-
-
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
-
14
-
-
0033833116
-
Protein structure alignment using environmental profiles
-
Jung,J. and Lee,B. (2000) Protein structure alignment using environmental profiles. Protein Eng., 13, 535-543.
-
(2000)
Protein Eng.
, vol.13
, pp. 535-543
-
-
Jung, J.1
Lee, B.2
-
15
-
-
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
-
16
-
-
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
-
18
-
-
4344656723
-
Approximate protein structural alignment in polynomial time
-
Kolodny,R. and Linial,N. (2004) Approximate protein structural alignment in polynomial time. Proc. Natl Acad. Sci. USA, 101, 12201-12206.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 12201-12206
-
-
Kolodny, R.1
Linial, N.2
-
19
-
-
0028015988
-
The protein threading problem with sequence amino acid interaction preferences is NP-complete
-
Lathrop,R.H. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7, 1059-1068.
-
(1994)
Protein Eng.
, vol.7
, pp. 1059-1068
-
-
Lathrop, R.H.1
-
20
-
-
78650670093
-
Maximum cliques in protein structure comparison. In
-
of Lecture Notes in Computer Science Springer, Berlin/Heidelberg
-
Malod-Dognin,N. et al. (2010) Maximum cliques in protein structure comparison. In Proceedings of the 9th International Symposium on Experimental Algorithms (SEA'10), Vol. 6049 of Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 106-117.
-
(2010)
Proceedings of the 9th International Symposium on Experimental Algorithms (SEA'10)
, vol.6049
, pp. 106-117
-
-
Malod-Dognin, N.1
-
21
-
-
34548304928
-
Comparative analysis of protein structure alignments
-
Mayr,G. et al. (2007) Comparative analysis of protein structure alignments. BMC Struct. Biol., 7, 50.
-
(2007)
BMC Struct. Biol.
, vol.7
, pp. 50
-
-
Mayr, G.1
-
22
-
-
38949150854
-
Matt: local flexibility aids protein multiple structure alignment
-
Menke,M. et al. (2008) Matt: local flexibility aids protein multiple structure alignment. PLoS Comput. Biol., 4, e10.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Menke, M.1
-
23
-
-
0031766401
-
HOMSTRAD: a database of protein structure alignments for homologous families
-
Mizuguchi,K. et al. (1998) HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci., 7, 2469-2471.
-
(1998)
Protein Sci.
, vol.7
, pp. 2469-2471
-
-
Mizuguchi, K.1
-
24
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame,C. et al. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
-
25
-
-
42549103756
-
A simple and fast heuristic for protein structure comparison
-
Pelta,D.A. et al. (2008) A simple and fast heuristic for protein structure comparison. BMC Bioinformatics, 9, 161.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 161
-
-
Pelta, D.A.1
-
26
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen,E.F. et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
-
27
-
-
0033564203
-
Molecular basis of glutathione synthetase deficiency and a rare gene permutation event
-
Polekhina,G. et al. (1999) Molecular basis of glutathione synthetase deficiency and a rare gene permutation event. EMBO J., 18, 3204-3213.
-
(1999)
EMBO J.
, vol.18
, pp. 3204-3213
-
-
Polekhina, G.1
-
28
-
-
70350682039
-
Algorithms for optimal protein structure alignment
-
Poleksic,A. (2009) Algorithms for optimal protein structure alignment. Bioinformatics, 25, 2751-2756.
-
(2009)
Bioinformatics
, vol.25
, pp. 2751-2756
-
-
Poleksic, A.1
-
29
-
-
67649221642
-
Flexible structural protein alignment by a sequence of local transformations
-
Rocha,J. et al. (2009) Flexible structural protein alignment by a sequence of local transformations. Bioinformatics, 25, 1625-1631.
-
(2009)
Bioinformatics
, vol.25
, pp. 1625-1631
-
-
Rocha, J.1
-
30
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
31
-
-
9944251424
-
Déjà vu all over again: finding and analyzing protein structure similarities
-
Sierk,M.L. and Kleywegt,G.J. (2004) Déjà vu all over again: finding and analyzing protein structure similarities. Structure, 12, 2103-2111.
-
(2004)
Structure
, vol.12
, pp. 2103-2111
-
-
Sierk, M.L.1
Kleywegt, G.J.2
-
32
-
-
34248201703
-
ASH structure alignment package: sensitivity and selectivity in domain classification
-
Standley,D.M. et al. (2007)ASH structure alignment package: sensitivity and selectivity in domain classification. BMC Bioinformatics, 8, 116.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 116
-
-
Standley, D.M.1
-
33
-
-
25144463996
-
Optimal protein structure alignment using maximum cliques
-
Strickland,D.M. et al. (2005) Optimal protein structure alignment using maximum cliques. Oper. Res., 53, 389-402.
-
(2005)
Oper. Res.
, vol.53
, pp. 389-402
-
-
Strickland, D.M.1
-
34
-
-
0000840656
-
Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core
-
Subbiah,S. et al. (1993) Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr. Biol., 3, 141-148.
-
(1993)
Curr. Biol.
, vol.3
, pp. 141-148
-
-
Subbiah, S.1
-
35
-
-
0024349252
-
Protein structure alignment
-
Taylor,W.R. and Orengo,C.A. (1989) Protein structure alignment. J. Mol. Biol., 208, 1-22.
-
(1989)
J. Mol. Biol.
, vol.208
, pp. 1-22
-
-
Taylor, W.R.1
Orengo, C.A.2
-
37
-
-
34447288497
-
A reduction-based exact algorithm for the contact map overlap problem
-
Xie,W. and Sahinidis,N.V. (2007) A reduction-based exact algorithm for the contact map overlap problem. J. Comput. Biol., 14, 637-654.
-
(2007)
J. Comput. Biol.
, vol.14
, pp. 637-654
-
-
Xie, W.1
Sahinidis, N.V.2
-
38
-
-
1042275611
-
Structural proteomics: a tool for genome annotation
-
Yakunin,A.F. et al. (2004) Structural proteomics: a tool for genome annotation. Curr. Opin. Chem. Biol., 8, 42-48.
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 42-48
-
-
Yakunin, A.F.1
-
39
-
-
3042581007
-
Flexible structure alignment by chaining aligned fragment pairs allowing twists
-
Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19 (Suppl. 2), 246-255.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
, pp. 246-255
-
-
Ye, Y.1
Godzik, A.2
-
40
-
-
0042622381
-
LGA: amethod for finding 3D similarities in protein structures
-
Zemla,A. (2003) LGA: amethod for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
41
-
-
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
|