-
2
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 233, 123-123 (1993).
-
(1993)
Journal of Molecular Biology
, vol.233
, pp. 123-123
-
-
Holm, L.1
Sander, C.2
-
3
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
DOI 10.1107/S0907444904026460
-
Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D: Biological Crystallography 60, 2256-2268 (2004). (Pubitemid 41742778)
-
(2004)
Acta Crystallographica Section D: Biological Crystallography
, vol.60
, Issue.12 I
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
4
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I. N. & Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein engineering 11, 739 (1998).
-
(1998)
Protein Engineering
, vol.11
, pp. 739
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
5
-
-
0024349252
-
Protein structure alignment
-
DOI 10.1016/0022-2836(89)90084-3
-
Taylor, W. R. & Orengo, C. A. Protein structure alignment. Journal of Molecular Biology 208, 1-22 (1989). (Pubitemid 19191513)
-
(1989)
Journal of Molecular Biology
, vol.208
, Issue.1
, pp. 1-22
-
-
Taylor, W.R.1
Orengo, C.A.2
-
6
-
-
44049099330
-
CLePAPS fast pair alignment of protein structures based on conformational letters
-
Wang, S. & Zheng, W. CLePAPS: fast pair alignment of protein structures based on conformational letters. Journal of bioinformatics and computational biology 6, 347 (2008).
-
(2008)
Journal of Bioinformatics and Computational Biology
, vol.6
, pp. 347
-
-
Wang, S.1
Zheng, W.2
-
7
-
-
3242887315
-
FATCAT a web server for flexible structure comparison and structure similarity searching
-
Ye, Y. & Godzik, A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic acids research 32, W582 (2004).
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Ye, Y.1
Godzik, A.2
-
8
-
-
12944271968
-
FAST: A novel protein structure alignment algorithm
-
DOI 10.1002/prot.20331
-
Zhu, J. & Weng, Z. FAST: a novel protein structure alignment algorithm. Proteins: Structure, Function, and Bioinformatics 58, 618-627 (2005). (Pubitemid 40176034)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.58
, Issue.3
, pp. 618-627
-
-
Zhu, J.1
Weng, Z.2
-
9
-
-
0033833116
-
Protein structure alignment using environmental profiles
-
Jung, J. & Lee, B. Protein structure alignment using environmental profiles. Protein Engineering 13, 535-543 (2000).
-
(2000)
Protein Engineering
, vol.13
, pp. 535-543
-
-
Jung, J.1
Lee, B.2
-
10
-
-
0003301367
-
The VAST protein structure comparison method
-
Gibrat, J., Madej, T., Spouge, J. & Bryant, S. The VAST protein structure comparison method. Biophys J 72, 298 (1997).
-
(1997)
Biophys J
, vol.72
, pp. 298
-
-
Gibrat, J.1
Madej, T.2
Spouge, J.3
Bryant, S.4
-
11
-
-
3242882573
-
CE-MC: Amultiple protein structure alignment server
-
Guda, C., Lu, S., Scheeff, E. D., Bourne, P. E.&Shindyalov, I. N. CE-MC: amultiple protein structure alignment server. Nucleic acids research 32, W100 (2004).
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Guda, C.1
Lu, S.2
Scheeff, E.D.3
Bourne, P.E.4
Shindyalov, I.N.5
-
12
-
-
33746218852
-
MUSTANG: A multiple structural alignment algorithm
-
DOI 10.1002/prot.20921
-
Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J. & Lesk, A. M. MUSTANG: a multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics 64, 559-574 (2006). (Pubitemid 44100724)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.3
, pp. 559-574
-
-
Konagurthu, A.S.1
Whisstock, J.C.2
Stuckey, P.J.3
Lesk, A.M.4
-
13
-
-
25144458667
-
A new progressive-iterative algorithm for multiple structure alignment
-
Lupyan, D., Leo-Macias, A. & Ortiz, A. R. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 21, 3255 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 3255
-
-
Lupyan, D.1
Leo-Macias, A.2
Ortiz, A.R.3
-
14
-
-
38949150854
-
Local flexibility aids protein multiple structure alignment
-
Menke, M., Berger, B. & Cowen, L. Matt: local flexibility aids protein multiple structure alignment. PLoS computational biology 4, e10 (2008).
-
(2008)
PLoS Computational Biology
, vol.4
-
-
Menke, M.1
Berger, B.2
Matt, C.L.3
-
15
-
-
80052693672
-
Alignment of distantly related protein structures: Algorithm, bound and implications to homology modeling
-
Wang, S., Peng, J. & Xu, J. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics 27, 2537-2545 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2537-2545
-
-
Wang, S.1
Peng, J.2
Xu, J.3
-
16
-
-
80052720106
-
Fast multiple alignment of protein structures using conformational letter blocks
-
Wang, S. & Zheng, W. M. Fast Multiple Alignment of Protein Structures Using Conformational Letter Blocks. Open Bioinformatics Journal 3, 69-83 (2009).
-
(2009)
Open Bioinformatics Journal
, vol.3
, pp. 69-83
-
-
Wang, S.1
Zheng, W.M.2
-
17
-
-
19544388989
-
Multiple flexible structure alignment using partial order graphs
-
Ye, Y. & Godzik, A. Multiple flexible structure alignment using partial order graphs. Bioinformatics 21, 2362 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 2362
-
-
Ye, Y.1
Godzik, A.2
-
18
-
-
34548304928
-
Comparative analysis of protein structure alignments
-
Mayr, G., Domingues, F. & Lackner, P. Comparative analysis of protein structure alignments. BMC Structural Biology 7, 50 (2007).
-
(2007)
BMC Structural Biology
, vol.7
, pp. 50
-
-
Mayr, G.1
Domingues, F.2
Lackner, P.3
-
19
-
-
17644392830
-
TM-align a protein structure alignment algorithm based on the TM-score
-
Zhang, Y. & Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research 33, 2302 (2005).
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 2302
-
-
Zhang, Y.1
Skolnick, J.2
-
20
-
-
35448992938
-
Accuracy of structure-based sequence alignment of automatic methods
-
Kim, C. & Lee, B. Accuracy of structure-based sequence alignment of automatic methods. BMC bioinformatics 8, 355 (2007).
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 355
-
-
Kim, C.1
Lee, B.2
-
21
-
-
84866980473
-
Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment
-
Nadimpalli, S., Daniels, N. & Cowen, L. Formatt: Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment. BMC Bioinformatics 13, 259 (2012).
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 259
-
-
Nadimpalli, S.1
Daniels, N.2
Formatt, C.L.3
-
23
-
-
42449090264
-
PROMALS3D: A tool for multiple protein sequence and structure alignments
-
Pei, J., Kim, B. H. & Grishin, N. V. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic acids research 36, 2295 (2008).
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 2295
-
-
Pei, J.1
Kim, B.H.2
Grishin, N.V.3
-
24
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
DOI 10.1016/j.jmb.2004.04.058, PII S0022283604005212
-
O'Sullivan, O., Suhre, K., Abergel, C., Higgins, D. G. & Notredame, C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. Journal of molecular biology 340, 385-395 (2004). (Pubitemid 38759917)
-
(2004)
Journal of Molecular Biology
, vol.340
, Issue.2
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
25
-
-
49949086495
-
The use of a conformational alphabet for fast alignment of protein structures
-
Zheng, W. M. The use of a conformational alphabet for fast alignment of protein structures. Bioinformatics Research and Applications, 331-342 (2008).
-
(2008)
Bioinformatics Research and Applications
, pp. 331-342
-
-
Zheng, W.M.1
-
27
-
-
16344394781
-
SABmark-A benchmark for sequence alignment that covers the entire known fold space
-
Van Walle, I., Lasters, I. & Wyns, L. SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 21, 1267 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 1267
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
28
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
DOI 10.1002/prot.20264
-
Zhang, Y. & Skolnick, J. Scoring function for automated assessment of protein structure template quality. Proteins: Structure, Function, and Bioinformatics 57, 702-710 (2004). (Pubitemid 39626992)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
29
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
DOI 10.1093/nar/gkg571
-
Zemla, A. LGA: amethod for finding 3D similarities in protein structures. Nucleic acids research 31, 3370-3374 (2003). (Pubitemid 37442162)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3370-3374
-
-
Zemla, A.1
-
30
-
-
0032568649
-
A unified statistical framework for sequence comparison and structure comparison
-
Levitt, M. &Gerstein,M.A unified statistical framework for sequence comparison and structure comparison. Proceedings of the National Academy of sciences 95, 5913 (1998).
-
(1998)
Proceedings of the National Academy of Sciences
, vol.95
, pp. 5913
-
-
Levitt, M.1
Gerstein, M.2
-
31
-
-
13444262384
-
CDD: A Conserved Domain Database for protein classification
-
Marchler-Bauer, A. et al. CDD: a Conserved Domain Database for protein classification. Nucleic acids research 33, D192 (2005).
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Marchler-Bauer, A.1
-
32
-
-
39749153446
-
MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs
-
DOI 10.1002/prot.21783
-
Cheng, H., Kim, B. H. & Grishin, N. V. MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs. Proteins: Structure, Function, and Bioinformatics 70, 1162-1166 (2008). (Pubitemid 351304076)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.4
, pp. 1162-1166
-
-
Cheng, H.1
Kim, B.-H.2
Grishin, N.V.3
-
33
-
-
38549170925
-
MALISAM: A database of structurally analogous motifs in proteins
-
Cheng, H., Kim, B. H. & Grishin, N. V. MALISAM: a database of structurally analogous motifs in proteins. Nucleic acids research 36, D211 (2008).
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Cheng, H.1
Kim, B.H.2
Grishin, N.V.3
-
34
-
-
67949111155
-
Iterative refinement of structure-based sequence alignments by Seed Extension
-
Kim, C., Tai, C. H. & Lee, B. Iterative refinement of structure-based sequence alignments by Seed Extension. BMC bioinformatics 10, 210 (2009).
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 210
-
-
Kim, C.1
Tai, C.H.2
Lee, B.3
-
35
-
-
3242880478
-
Fold Miner and LOCK 2: Protein structure comparison and motif discovery on the web
-
Shapiro, J. & Brutlag, D. FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. Nucleic acids research 32, W536 (2004).
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Shapiro, J.1
Brutlag, D.2
-
36
-
-
0041620359
-
MATRAS a program for protein 3D structure comparison
-
Kawabata, T. MATRAS: a program for protein 3D structure comparison. Nucleic acids research 31, 3367 (2003).
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3367
-
-
Kawabata, T.1
-
37
-
-
0028961335
-
SCOP a structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of molecular biology 247, 536-540 (1995).
-
(1995)
Journal of Molecular Biology
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
38
-
-
40849133659
-
Discrimination between distant homologs and structural analogs: Lessons from manually constructed, reliable data sets
-
Cheng, H., Kim, B. H. & Grishin, N. V. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. Journal of molecular biology 377, 1265-1278 (2008).
-
(2008)
Journal of Molecular Biology
, vol.377
, pp. 1265-1278
-
-
Cheng, H.1
Kim, B.H.2
Grishin, N.V.3
-
39
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
-
Moult, J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Current opinion in structural biology 15, 285-289 (2005). (Pubitemid 40826447)
-
(2005)
Current Opinion in Structural Biology
, vol.15
, Issue.3 SPEC. ISSUE
, pp. 285-289
-
-
Moult, J.1
-
40
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
DOI 10.1093/nar/gki408
-
Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic acids research 33, W244-W248 (2005). (Pubitemid 44529917)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISSUE
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
41
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25, 3389 (1997).
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 3389
-
-
Altschul, S.F.1
-
42
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 951
-
-
Söding, J.1
-
43
-
-
44449139387
-
Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
-
Xie, L. & Bourne, P. E. Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proceedings of the National Academy of sciences 105, 5441 (2008).
-
(2008)
Proceedings of the National Academy of Sciences
, vol.105
, pp. 5441
-
-
Xie, L.1
Bourne, P.E.2
-
44
-
-
38349100452
-
A threading-based method (FINDSITE) for ligandbinding site prediction and functional annotation
-
Brylinski, M. & Skolnick, J. A threading-based method (FINDSITE) for ligandbinding site prediction and functional annotation. Proceedings of the National Academy of sciences 105, 129 (2008).
-
(2008)
Proceedings of the National Academy of Sciences
, vol.105
, pp. 129
-
-
Brylinski, M.1
Skolnick, J.2
-
45
-
-
77956502131
-
IAlign: A method for the structural comparison of protein-protein interfaces
-
Gao, M. & Skolnick, J. iAlign: a method for the structural comparison of protein-protein interfaces. Bioinformatics 26, 2259 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2259
-
-
Gao, M.1
Skolnick, J.2
-
48
-
-
0027991446
-
The FSSP database of structurally aligned protein fold families
-
Holm, L. & Sander, C. The FSSP database of structurally aligned protein fold families. Nucleic acids research 22, 3600 (1994).
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 3600
-
-
Holm, L.1
Sander, C.2
-
49
-
-
77951961719
-
How significant is a protein structure similarity with TMscore5 0.5?
-
Xu, J. & Zhang, Y. How significant is a protein structure similarity with TMscore5 0.5? Bioinformatics 26, 889-895 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 889-895
-
-
Xu, J.1
Zhang, Y.2
-
51
-
-
0034495586
-
ProSup: A refined tool for protein structure alignment
-
Lackner, P., Koppensteiner, W. A., Sippl, M. J. & Domingues, F. S. ProSup: a refined tool for protein structure alignment. Protein Engineering 13, 745 (2000).
-
(2000)
Protein Engineering
, vol.13
, pp. 745
-
-
Lackner, P.1
Koppensteiner, W.A.2
Sippl, M.J.3
Domingues, F.S.4
|