-
1
-
-
0030464952
-
Detection of non-topological motifs in protein structures
-
Alesker, V. et al. (1996) Detection of non-topological motifs in protein structures. Protein Eng., 9, 1103-1119.
-
(1996)
Protein Eng.
, vol.9
, pp. 1103-1119
-
-
Alesker, V.1
-
2
-
-
38549153238
-
Data growth and its impact on the SCOP database: new developments
-
Andreeva, A. et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Andreeva, A.1
-
3
-
-
33747829924
-
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
-
Armougom, F. et al. (2006) Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res., 34 (Suppl. 2), W604-W608.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.SUPPL. 2
-
-
Armougom, F.1
-
4
-
-
33846704538
-
Vorolign-fast structural alignment using Voronoi contacts
-
Birzele, F. et al. (2007) Vorolign-fast structural alignment using Voronoi contacts. Bioinformatics, 23, E205-E211.
-
(2007)
Bioinformatics
, vol.23
-
-
Birzele, F.1
-
5
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
Brenner, S.E. et al. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 254-256
-
-
Brenner, S.E.1
-
6
-
-
77649240530
-
FragBag, an accurate representation of protein structure, retrieves structural neighbours from the entire PDB quickly and accurately
-
Budowski-Tal, I. et al. (2010) FragBag, an accurate representation of protein structure, retrieves structural neighbours from the entire PDB quickly and accurately. Proc. Natl Acad. Sci., 107, 3481-3486.
-
(2010)
Proc. Natl Acad. Sci.
, vol.107
, pp. 3481-3486
-
-
Budowski-Tal, I.1
-
7
-
-
34250830250
-
Recent progress in measuring structural similarity between proteins
-
Carugo, O. (2007) Recent progress in measuring structural similarity between proteins. Curr. Protein Pept. Sci., 8, 219-241.
-
(2007)
Curr. Protein Pept. Sci.
, vol.8
, pp. 219-241
-
-
Carugo, O.1
-
8
-
-
28844438017
-
A novel approach to structural alignment using realistic structural and environmental information
-
Chen, Y. and Crippen, G.M. (2005) A novel approach to structural alignment using realistic structural and environmental information. Protein Sci., 14, 2935-2946.
-
(2005)
Protein Sci
, vol.14
, pp. 2935-2946
-
-
Chen, Y.1
Crippen, G.M.2
-
9
-
-
0029936121
-
Suprising similarities in structure comparison
-
Gibrat, J.F. et al. (1996) Suprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 377-385
-
-
Gibrat, J.F.1
-
10
-
-
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
-
11
-
-
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
-
12
-
-
79959726138
-
Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold
-
Hollup, S.M. et al. (2011) Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. Comput. Biol. Chem., 35, 174-188.
-
(2011)
Comput. Biol. Chem.
, vol.35
, pp. 174-188
-
-
Hollup, S.M.1
-
13
-
-
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
-
14
-
-
79953300931
-
GOSSIP: amethod for fast and accurate global alignment of protein structures
-
Kifer, I. et al. (2011) GOSSIP: amethod for fast and accurate global alignment of protein structures. Bioinformatics, 27, 925-932.
-
(2011)
Bioinformatics
, vol.27
, pp. 925-932
-
-
Kifer, I.1
-
15
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
-
Kolodny, R. et al. (2005) Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol., 346, 1173-1188.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
-
16
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel, E. and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D., 60, 2256-2268.
-
(2004)
Acta Crystallogr. D.
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
17
-
-
0034495586
-
ProSup: a refined tool for protein structure alignment
-
Lackner, P. et al. (2000) ProSup: a refined tool for protein structure alignment. Protein Eng., 13, 745-752.
-
(2000)
Protein Eng.
, vol.13
, pp. 745-752
-
-
Lackner, P.1
-
18
-
-
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
-
19
-
-
78651274743
-
Superfamily 1.75 including a domain-centric gene ontology method
-
Morais, D.A.D.L. et al. (2011) Superfamily 1.75 including a domain-centric gene ontology method. Nucleic Acids Res., 39, D427-D434.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Morais, D.A.D.L.1
-
20
-
-
51849139041
-
Alignment of protein structures in the presence of domain motions
-
Mosca, R. et al. (2008) Alignment of protein structures in the presence of domain motions. BMC Bioinformatics, 9, 352.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 352
-
-
Mosca, R.1
-
21
-
-
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
-
22
-
-
78249258372
-
Searching protein 3D structures for optimal structure alignment using intelligent algorithms and data structures
-
Novosad, T. et al. (2010) Searching protein 3D structures for optimal structure alignment using intelligent algorithms and data structures. IEEE Trans. Inf. Technol. Biomed., 14, 1378-1386.
-
(2010)
IEEE Trans. Inf. Technol. Biomed.
, vol.14
, pp. 1378-1386
-
-
Novosad, T.1
-
23
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan, O. et al. (2004) 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol., 340, 385-395.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
-
24
-
-
84870685970
-
MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison
-
Ortiz, A.R. et al. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 21, 3255-3263.
-
(2002)
Protein Sci.
, vol.21
, pp. 3255-3263
-
-
Ortiz, A.R.1
-
25
-
-
58649097284
-
Fr-TM-align: a new protein structural alingment methods based on fragment alignments and the TM-score
-
Pandit, S.B. and Skolnick, J. (2008) Fr-TM-align: a new protein structural alingment methods based on fragment alignments and the TM-score. BMC Bioinformatics, 9, 531.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 531
-
-
Pandit, S.B.1
Skolnick, J.2
-
26
-
-
48449087960
-
PROMALS3D web server for accurate multiple protein sequence and structure alignments
-
Pei, J.M. et al. (2008) PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Res., 36, W30-W34.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Pei, J.M.1
-
27
-
-
0345864027
-
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
-
Porter, C.T. et al. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res., 32, D129-D133.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Porter, C.T.1
-
28
-
-
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
-
29
-
-
74949144511
-
Protein structures, folds and fold spaces
-
Sadowski, M.I. and Taylor, W.R. (2010a) Protein structures, folds and fold spaces. J. Phys. Condens. Matter, 22, 033103.
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 033103
-
-
Sadowski, M.I.1
Taylor, W.R.2
-
30
-
-
77958194276
-
On the evolutionary origins of "fold space continuity": a study of topological convergence and divergence in mixed alpha-beta domains
-
Sadowski, M.I. and Taylor, W.R. (2010b) On the evolutionary origins of "fold space continuity": a study of topological convergence and divergence in mixed alpha-beta domains. J. Struct. Biol., 172, 244-252.
-
(2010)
J. Struct. Biol.
, vol.172
, pp. 244-252
-
-
Sadowski, M.I.1
Taylor, W.R.2
-
31
-
-
77951197269
-
FlexSnap: flexible non-sequential protein structure alignment
-
Salem, S. et al. (2010) FlexSnap: flexible non-sequential protein structure alignment. Algorithm. Mol. Biol., 5, 12.
-
(2010)
Algorithm. Mol. Biol.
, vol.5
, pp. 12
-
-
Salem, S.1
-
32
-
-
0017386137
-
Recognition of phylogenetic relationships from polypeptide chain fold similarities
-
Schulz, G.E. (1977) Recognition of phylogenetic relationships from polypeptide chain fold similarities. J. Mol. Evol., 9, 339-342.
-
(1977)
J. Mol. Evol.
, vol.9
, pp. 339-342
-
-
Schulz, G.E.1
-
33
-
-
1842450688
-
FlexProt: alignment of flexible protein structures without a predefinition of hinge regions
-
Shatsky, M. et al. (2004) FlexProt: alignment of flexible protein structures without a predefinition of hinge regions. J. Comput. Biol., 11, 83-106.
-
(2004)
J. Comput. Biol.
, vol.11
, pp. 83-106
-
-
Shatsky, M.1
-
34
-
-
79957583831
-
A spectral approach to protein structure alignment
-
Shibberu, Y. and Holder, A. (2011) A spectral approach to protein structure alignment. IEEE Trans. Comput. Biol. Bioinf., 8, 867-875.
-
(2011)
IEEE Trans. Comput. Biol. Bioinf.
, vol.8
, pp. 867-875
-
-
Shibberu, Y.1
Holder, A.2
-
35
-
-
3142745171
-
Alternative alignments from comparison of protein structures
-
Shih, E.S.C. and Hwang, M.J. (2004) Alternative alignments from comparison of protein structures. Proteins, 56, 519-527.
-
(2004)
Proteins
, vol.56
, pp. 519-527
-
-
Shih, E.S.C.1
Hwang, M.J.2
-
36
-
-
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. Prot. Eng., 11, 739-747.
-
(1998)
Prot. Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
37
-
-
0033011876
-
Protein structure comparison using iterated double dynamic programming
-
Taylor, W.R. (1999) Protein structure comparison using iterated double dynamic programming. Protein Sci., 8, 654-665.
-
(1999)
Protein Sci
, vol.8
, pp. 654-665
-
-
Taylor, W.R.1
-
38
-
-
84885550227
-
Protein products of tandem gene duplication: a structural view
-
Dittmar, K. and Liberles, D. (eds) Wiley-Blackwell, Hoboken, NJ
-
Taylor, W.R. and Sadowski, M.I. (2010) Protein products of tandem gene duplication: a structural view. In Dittmar, K. and Liberles, D. (eds) Evolution After Gene Duplication. Wiley-Blackwell, Hoboken, NJ, pp. 133-163.
-
(2010)
Evolution After Gene Duplication
, pp. 133-163
-
-
Taylor, W.R.1
Sadowski, M.I.2
-
39
-
-
0033631725
-
Multiple protein sequence alignment using double-dynamic programming
-
Taylor, W.R. et al. (2000) Multiple protein sequence alignment using double-dynamic programming. Comput. Chem., 24, 3-12.
-
(2000)
Comput. Chem.
, vol.24
, pp. 3-12
-
-
Taylor, W.R.1
-
40
-
-
0036221375
-
A Fourier analysis of symmetry in protein structure
-
Taylor, W.R. et al. (2002) A Fourier analysis of symmetry in protein structure. Prot. Eng., 15, 79-89.
-
(2002)
Prot. Eng.
, vol.15
, pp. 79-89
-
-
Taylor, W.R.1
-
41
-
-
52749091256
-
TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ strings model
-
Veeramalai, M. et al. (2009) TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ strings model. BMC Bioinformatics, 9, 358.
-
(2009)
BMC Bioinformatics
, vol.9
, pp. 358
-
-
Veeramalai, M.1
-
42
-
-
33644869455
-
Flexible secondary structure based protein structure comparison applied to the detection of circular permutation
-
Vesterstrom, J. and Taylor, W.R. (2006) Flexible secondary structure based protein structure comparison applied to the detection of circular permutation. J. Comput. Biol., 13, 43-62.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 43-62
-
-
Vesterstrom, J.1
Taylor, W.R.2
-
43
-
-
3042581007
-
Flexible structure alignment by chaining aligned fragment pairs allowing twists
-
Ye, Y.Z. and Godzik, A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19, ii246-ii255.
-
(2003)
Bioinformatics
, vol.19
-
-
Ye, Y.Z.1
Godzik, A.2
-
44
-
-
10344232638
-
Scoring function for the assessment of protein structure template quality
-
Zhang, Y. and Skolnick, J. (2004) Scoring function for the assessment of protein structure template quality. Proteins, 52, 702-710.
-
(2004)
Proteins
, vol.52
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
45
-
-
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
|