-
1
-
-
0032545151
-
Estimating the number of protein folds
-
10.1006/jmbi.1998.2282. 9878351
-
Estimating the number of protein folds. C Zhang C DeLisi, J Mol Biol 1998 284 5 1301 1305 10.1006/jmbi.1998.2282 9878351
-
(1998)
J Mol Biol
, vol.284
, Issue.5
, pp. 1301-1305
-
-
Zhang, C.1
Delisi, C.2
-
2
-
-
0033574401
-
Correlation of observed fold frequency with the occurrence of local structural motifs
-
10.1006/jmbi.1999.2642. 10222204
-
Correlation of observed fold frequency with the occurrence of local structural motifs. GM Salem EG Hutchinson CA Orengo JM Thornton, J Mol Biol 1999 287 5 969 981 10.1006/jmbi.1999.2642 10222204
-
(1999)
J Mol Biol
, vol.287
, Issue.5
, pp. 969-981
-
-
Salem, G.M.1
Hutchinson, E.G.2
Orengo, C.A.3
Thornton, J.M.4
-
3
-
-
0035896377
-
The TIM-barrel fold: A versatile framework for efficient enzymes
-
10.1016/S0014-5793(01)02236-0. 11257493
-
The TIM-barrel fold:a versatile framework for efficient enzymes. RK Wierenga, FEBS Lett 2001 492 3 193 198 10.1016/S0014-5793(01)02236-0 11257493
-
(2001)
FEBS Lett
, vol.492
, Issue.3
, pp. 193-198
-
-
Wierenga, R.K.1
-
4
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
7723011
-
SCOP:a structural classification of proteins database for the investigation of sequences and structures. AG Murzin SE Brenner T Hubbard C Chothia, J Mol Biol 1995 247 4 536 540 7723011
-
(1995)
J Mol Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
5
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
10.1016/S0022-2836(02)00649-6. 12206759
-
One fold with many functions:the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. N Nagano CA Orengo JM Thornton, J Mol Biol 2002 321 5 741 765 10.1016/S0022-2836(02)00649-6 12206759
-
(2002)
J Mol Biol
, vol.321
, Issue.5
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
6
-
-
0038486929
-
An evolutionarily structured universe of protein architecture
-
10.1101/gr.1161903. 12840035
-
An evolutionarily structured universe of protein architecture. G Caetano-Anolles D Caetano-Anolles, Genome Res 2003 13 7 1563 1571 10.1101/gr.1161903 12840035
-
(2003)
Genome Res
, vol.13
, Issue.7
, pp. 1563-1571
-
-
Caetano-Anolles, G.1
Caetano-Anolles, D.2
-
8
-
-
0023989064
-
Improved tools for biological sequence comparison
-
10.1073/pnas.85.8.2444. 3162770
-
Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proc Natl Acad Sci USA 1988 85 8 2444 2448 10.1073/pnas.85.8.2444 3162770
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, Issue.8
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
9
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
10.1093/nar/25.17.3389. 9254694
-
Gapped BLAST and PSI-BLAST:a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
10
-
-
0030925920
-
Pfam: A comprehensive database of protein domain families based on seed alignments
-
10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L. 9223186
-
Pfam: a comprehensive database of protein domain families based on seed alignments. EL Sonnhammer SR Eddy R Durbin, Proteins 1997 28 3 405 420 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L 9223186
-
(1997)
Proteins
, vol.28
, Issue.3
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
11
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
10716175
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information. L Rychlewski L Jaroszewski WZ Li A Godzik, Protein Sci 2000 9 2 232 241 10716175
-
(2000)
Protein Sci
, vol.9
, Issue.2
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.Z.3
Godzik, A.4
-
12
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
10.1006/jmbi.2000.3741. 10860755
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM. LA Kelley RM MacCallum MJE Sternberg, Journal of Molecular Biology 2000 299 2 499 520 10.1006/jmbi.2000.3741 10860755
-
(2000)
Journal of Molecular Biology
, vol.299
, Issue.2
, pp. 499-520
-
-
Kelley, L.A.1
MacCallum, R.M.2
Sternberg, M.J.E.3
-
13
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
10.1006/jmbi.2001.4762. 11419950
-
FUGUE:sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Shi TL Blundell K Mizuguchi, J Mol Biol 2001 310 1 243 257 10.1006/jmbi.2001.4762 11419950
-
(2001)
J Mol Biol
, vol.310
, Issue.1
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
14
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
10.1093/bioinformatics/btg097. 12724298
-
Improvement of the GenTHREADER method for genomic fold recognition. LJ McGuffin DT Jones, Bioinformatics 2003 19 7 874 881 10.1093/bioinformatics/ btg097 12724298
-
(2003)
Bioinformatics
, vol.19
, Issue.7
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
15
-
-
0042121000
-
ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
-
10.1093/nar/gkg504. 12824423
-
ORFeus:detection of distant homology using sequence profiles and predicted secondary structure. K Ginalski J Pas LS Wyrwicz M von Grotthuss JM Bujnicki L Rychlewski, Nucleic Acids Research 2003 31 13 3804 3807 10.1093/nar/gkg504 12824423
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3804-3807
-
-
Ginalski, K.1
Pas, J.2
Wyrwicz, L.S.3
Von Grotthuss, M.4
Bujnicki, J.M.5
Rychlewski, L.6
-
16
-
-
36749103110
-
Automated server predictions in CASP7
-
10.1002/prot.21761. 17894354
-
Automated server predictions in CASP7. JN Battey J Kopp L Bordoli RJ Read ND Clarke T Schwede, Proteins 2007 69 Suppl 8 68 82 10.1002/prot.21761 17894354
-
(2007)
Proteins
, vol.69
, Issue.SUPPL 8
, pp. 68-82
-
-
Battey, J.N.1
Kopp, J.2
Bordoli, L.3
Read, R.J.4
Clarke, N.D.5
Schwede, T.6
-
17
-
-
11144241105
-
LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
-
10.1110/ps.04888805. 15608124
-
LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. L Rychlewski D Fischer, Protein Sci 2005 14 1 240 245 10.1110/ps.04888805 15608124
-
(2005)
Protein Sci
, vol.14
, Issue.1
, pp. 240-245
-
-
Rychlewski, L.1
Fischer, D.2
-
18
-
-
0033625972
-
Profiles from structure based sequence alignment of porins can identify beta stranded integral membrane proteins
-
10.1093/bioinformatics/16.9.839. 11108707
-
Profiles from structure based sequence alignment of porins can identify beta stranded integral membrane proteins. TV Gnanasekaran S Peri A Arockiasamy S Krishnaswamy, Bioinformatics 2000 16 9 839 842 10.1093/bioinformatics/16.9.839 11108707
-
(2000)
Bioinformatics
, vol.16
, Issue.9
, pp. 839-842
-
-
Gnanasekaran, T.V.1
Peri, S.2
Arockiasamy, A.3
Krishnaswamy, S.4
-
19
-
-
0036708003
-
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
-
10.1110/ps.0209002. 12192075
-
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Y Zhai MH Saier Jr, Protein Sci 2002 11 9 2196 2207 10.1110/ps.0209002 12192075
-
(2002)
Protein Sci
, vol.11
, Issue.9
, pp. 2196-2207
-
-
Zhai, Y.1
Saier Jr., M.H.2
-
20
-
-
43249097732
-
TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles
-
10.1016/j.compbiolchem.2008.03.002. 18434251
-
TMBETADISC-RBF:Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. YY Ou MM Gromiha SA Chen M Suwa, Comput Biol Chem 2008 32 3 227 231 10.1016/j.compbiolchem.2008.03.002 18434251
-
(2008)
Comput Biol Chem
, vol.32
, Issue.3
, pp. 227-231
-
-
Ou, Y.Y.1
Gromiha, M.M.2
Chen, S.A.3
Suwa, M.4
-
21
-
-
2642587355
-
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods
-
10.1002/prot.20092. 15162482
-
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. NK Natt H Kaur GP Raghava, Proteins 2004 56 1 11 18 10.1002/prot.20092 15162482
-
(2004)
Proteins
, vol.56
, Issue.1
, pp. 11-18
-
-
Natt, N.K.1
Kaur, H.2
Raghava, G.P.3
-
22
-
-
62449292145
-
In silico identification of novel G protein coupled receptors
-
full-text. 19153682
-
In silico identification of novel G protein coupled receptors. MN Davies DR Flower, Methods Mol Biol 2009 528 25 36 full-text 19153682
-
(2009)
Methods Mol Biol
, vol.528
, pp. 25-36
-
-
Davies, M.N.1
Flower, D.R.2
-
23
-
-
68149164782
-
7TMRmine: A Web server for hierarchical mining of 7TMR proteins
-
10.1186/1471-2164-10-275. 19538753
-
7TMRmine:a Web server for hierarchical mining of 7TMR proteins. G Lu Z Wang AM Jones EN Moriyama, BMC Genomics 2009 10 1 275 10.1186/1471-2164-10-275 19538753
-
(2009)
BMC Genomics
, vol.10
, Issue.1
, pp. 275
-
-
Lu, G.1
Wang, Z.2
Jones, A.M.3
Moriyama, E.N.4
-
24
-
-
61849129612
-
Combination of several bioinformatics approaches for the identification of new putative glycosyltransferases in Arabidopsis
-
10.1021/pr800808m. 19086785
-
Combination of several bioinformatics approaches for the identification of new putative glycosyltransferases in Arabidopsis. SF Hansen E Bettler M Wimmerova A Imberty O Lerouxel C Breton, J Proteome Res 2009 8 2 743 753 10.1021/pr800808m 19086785
-
(2009)
J Proteome Res
, vol.8
, Issue.2
, pp. 743-753
-
-
Hansen, S.F.1
Bettler, E.2
Wimmerova, M.3
Imberty, A.4
Lerouxel, O.5
Breton, C.6
-
25
-
-
13244289774
-
Descriptor-based protein remote homology identification
-
10.1110/ps.041035505. 15632283
-
Descriptor-based protein remote homology identification. Z Zhang S Kochhar MG Grigorov, Protein Sci 2005 14 2 431 444 10.1110/ps.041035505 15632283
-
(2005)
Protein Sci
, vol.14
, Issue.2
, pp. 431-444
-
-
Zhang, Z.1
Kochhar, S.2
Grigorov, M.G.3
-
26
-
-
0032944238
-
The PROSITE database, its status in 1999
-
10.1093/nar/27.1.215. 9847184
-
The PROSITE database, its status in 1999. K Hofmann P Bucher L Falquet A Bairoch, Nucleic Acids Res 1999 27 1 215 219 10.1093/nar/27.1.215 9847184
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.1
, pp. 215-219
-
-
Hofmann, K.1
Bucher, P.2
Falquet, L.3
Bairoch, A.4
-
27
-
-
0001969211
-
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
-
10.1016/S0097-8485(96)80004-0. 16718863
-
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. M Gribskov NL Robinson, Comput Chem 1996 20 1 25 33 10.1016/S0097-8485(96)80004-0 16718863
-
(1996)
Comput Chem
, vol.20
, Issue.1
, pp. 25-33
-
-
Gribskov, M.1
Robinson, N.L.2
-
28
-
-
36448960843
-
PFRES: Protein fold classification by using evolutionary information and predicted secondary structure
-
10.1093/bioinformatics/btm475. 17942446
-
PFRES:protein fold classification by using evolutionary information and predicted secondary structure. K Chen L Kurgan, Bioinformatics 2007 23 21 2843 2850 10.1093/bioinformatics/btm475 17942446
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2843-2850
-
-
Chen, K.1
Kurgan, L.2
-
29
-
-
13844292778
-
The SSEA server for protein secondary structure alignment
-
10.1093/bioinformatics/bti013. 15347578
-
The SSEA server for protein secondary structure alignment. P Fontana E Bindewald S Toppo R Velasco G Valle SC Tosatto, Bioinformatics 2005 21 3 393 395 10.1093/bioinformatics/bti013 15347578
-
(2005)
Bioinformatics
, vol.21
, Issue.3
, pp. 393-395
-
-
Fontana, P.1
Bindewald, E.2
Toppo, S.3
Velasco, R.4
Valle, G.5
Tosatto, S.C.6
-
30
-
-
0033056948
-
A protein taxonomy based on secondary structure
-
10.1038/10728. 10404226
-
A protein taxonomy based on secondary structure. T Przytycka R Aurora GD Rose, Nat Struct Biol 1999 6 7 672 682 10.1038/10728 10404226
-
(1999)
Nat Struct Biol
, vol.6
, Issue.7
, pp. 672-682
-
-
Przytycka, T.1
Aurora, R.2
Rose, G.D.3
-
31
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
10.1093/protein/11.9.739. 9796821
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. IN Shindyalov PE Bourne, Protein Eng 1998 11 9 739 747 10.1093/protein/11.9.739 9796821
-
(1998)
Protein Eng
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
32
-
-
0035191439
-
Motif-based fold assignment
-
11714913
-
Motif-based fold assignment. L Salwinski D Eisenberg, Protein Sci 2001 10 12 2460 2469 11714913
-
(2001)
Protein Sci
, vol.10
, Issue.12
, pp. 2460-2469
-
-
Salwinski, L.1
Eisenberg, D.2
-
33
-
-
58149307468
-
ESLpred2: Improved method for predicting subcellular localization of eukaryotic proteins
-
10.1186/1471-2105-9-503. 19038062
-
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins. A Garg GP Raghava, BMC Bioinformatics 2008 9 503 10.1186/1471-2105-9-503 19038062
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 503
-
-
Garg, A.1
Raghava, G.P.2
-
34
-
-
62249106701
-
Prediction of nuclear proteins using SVM and HMM models
-
10.1186/1471-2105-10-22. 19152693
-
Prediction of nuclear proteins using SVM and HMM models. M Kumar GP Raghava, BMC Bioinformatics 2009 10 22 10.1186/1471-2105-10-22 19152693
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 22
-
-
Kumar, M.1
Raghava, G.P.2
-
35
-
-
0141634358
-
Exploring the sequence-structure protein landscape in the glycosyltransferase family
-
10.1110/ps.03131303. 14500887
-
Exploring the sequence-structure protein landscape in the glycosyltransferase family. Z Zhang S Kochhar M Grigorov, Protein Sci 2003 12 10 2291 2302 10.1110/ps.03131303 14500887
-
(2003)
Protein Sci
, vol.12
, Issue.10
, pp. 2291-2302
-
-
Zhang, Z.1
Kochhar, S.2
Grigorov, M.3
-
36
-
-
27644455582
-
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
-
10.1186/1471-2105-6-253. 16225676
-
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. T Ohlson A Elofsson, BMC Bioinformatics 2005 6 253 10.1186/1471-2105-6-253 16225676
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 253
-
-
Ohlson, T.1
Elofsson, A.2
-
37
-
-
0033977581
-
The ASTRAL compendium for protein structure and sequence analysis
-
10.1093/nar/28.1.254. 10592239
-
The ASTRAL compendium for protein structure and sequence analysis. SE Brenner P Koehl M Levitt, Nucleic Acids Res 2000 28 1 254 256 10.1093/nar/28.1.254 10592239
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 254-256
-
-
Brenner, S.E.1
Koehl, P.2
Levitt, M.3
-
38
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
10.1093/bioinformatics/btl158. 16731699
-
Cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences. W Li A Godzik, Bioinformatics 2006 22 13 1658 1659 10.1093/bioinformatics/btl158 16731699
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
39
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
10.1006/jmbi.1999.3091. 10493868
-
Protein secondary structure prediction based on position-specific scoring matrices. DT Jones, J Mol Biol 1999 292 2 195 202 10.1006/jmbi.1999.3091 10493868
-
(1999)
J Mol Biol
, vol.292
, Issue.2
, pp. 195-202
-
-
Jones, D.T.1
-
40
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
10.1016/0022-2836(70)90057-4. 5420325
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins. SB Needleman CD Wunsch, J Mol Biol 1970 48 3 443 453 10.1016/0022-2836(70)90057-4 5420325
-
(1970)
J Mol Biol
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
41
-
-
0042622243
-
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
-
10.1093/nar/gkg600. 12824396
-
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. CZ Cai LY Han ZL Ji X Chen YZ Chen, Nucleic Acids Res 2003 31 13 3692 3697 10.1093/nar/gkg600 12824396
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3692-3697
-
-
Cai, C.Z.1
Han, L.Y.2
Ji, Z.L.3
Chen, X.4
Chen, Y.Z.5
-
42
-
-
0041743078
-
Distinguishing enzyme structures from non-enzymes without alignments
-
10.1016/S0022-2836(03)00628-4. 12850146
-
Distinguishing enzyme structures from non-enzymes without alignments. PD Dobson AJ Doig, J Mol Biol 2003 330 4 771 783 10.1016/S0022-2836(03)00628-4 12850146
-
(2003)
J Mol Biol
, vol.330
, Issue.4
, pp. 771-783
-
-
Dobson, P.D.1
Doig, A.J.2
|