-
1
-
-
2942576133
-
The interplay of fold recognition and experimental structure determination in structural genomics
-
Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol 2004;14:307-312.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 307-312
-
-
Friedberg, I.1
Jaroszewski, L.2
Ye, Y.3
Godzik, A.4
-
2
-
-
34347394165
-
Towards a comprehensive structural coverage of completed genomes: A structural genomics viewpoint
-
Marsden RL, Lewis TA, Orengo CA. Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC Bioinformatics 2007;8:86.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 86
-
-
Marsden, R.L.1
Lewis, T.A.2
Orengo, C.A.3
-
3
-
-
33747871139
-
A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory
-
Fox JA, McMillan S, Ouellette BFF. A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory. Nucleic Acids Res 2006;34(Suppl 2):W3-W5.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.SUPPL. 2
-
-
Fox, J.A.1
McMillan, S.2
Ouellette, B.F.F.3
-
4
-
-
9144244232
-
-
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004;32(Suppl 1):D217-D222.
-
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 2004;32(Suppl 1):D217-D222.
-
-
-
-
5
-
-
33644874606
-
The SWISS-MODEL repository: New features and functionalities
-
Kopp J, Schwede T. The SWISS-MODEL repository: new features and functionalities. Nucleic Acids Res 2006;34(Suppl 1):D315-D318.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.SUPPL. 1
-
-
Kopp, J.1
Schwede, T.2
-
6
-
-
33644877685
-
-
Castrignano T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. The PMDB protein model database. Nucleic Acids Res 2006;34 (Database Issue):D306-D309.
-
Castrignano T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. The PMDB protein model database. Nucleic Acids Res 2006;34 (Database Issue):D306-D309.
-
-
-
-
7
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 2005;15:285-289.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 285-289
-
-
Moult, J.1
-
8
-
-
0032606140
-
CAFASP-1: Critical assessment of fully automated structure prediction methods
-
Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins 1999;(Suppl 3):209-217.
-
(1999)
Proteins
, Issue.SUPPL. 3
, pp. 209-217
-
-
Fischer, D.1
Barret, C.2
Bryson, K.3
Elofsson, A.4
Godzik, A.5
Jones, D.6
Karplus, K.J.7
Kelley, L.A.8
MacCallum, R.M.9
Pawowski, K.10
Rost, B.11
Rychlewski, L.12
Sternberg, M.13
-
9
-
-
0242299155
-
CAFASP3: The third critical assessment of fully automated structure prediction methods
-
Fischer D, Rychlewski L, Dunbrack RL, Jr, Ortiz AR, Elofsson A. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 2003;53(Suppl 6):503-516.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 503-516
-
-
Fischer, D.1
Rychlewski, L.2
Dunbrack Jr, R.L.3
Ortiz, A.R.4
Elofsson, A.5
-
10
-
-
30344459116
-
Critical assessment of methods of protein structure prediction (CASP)-round 6
-
Moult J, Fidelis K, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round 6. Proteins 2005;61(Suppl 7):3-7.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 3-7
-
-
Moult, J.1
Fidelis, K.2
Rost, B.3
Hubbard, T.4
Tramontano, A.5
-
11
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61(Suppl 7):225-236.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
12
-
-
0035747672
-
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
-
Bates PA, Kelley LA, MacCallum RM, Sternberg MJ. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 2001;45(Suppl 5):39-46.
-
(2001)
Proteins
, vol.45
, Issue.SUPPL. 5
, pp. 39-46
-
-
Bates, P.A.1
Kelley, L.A.2
MacCallum, R.M.3
Sternberg, M.J.4
-
13
-
-
33747854222
-
Developing a move-set for protein model refinement
-
Offman MN, Fitzjohn PW, Bates PA. Developing a move-set for protein model refinement. Bioinformatics 2006;22:1838-1845.
-
(2006)
Bioinformatics
, vol.22
, pp. 1838-1845
-
-
Offman, M.N.1
Fitzjohn, P.W.2
Bates, P.A.3
-
14
-
-
0242299188
-
Novel use of a genetic algorithm for protein structure prediction: Searching template and sequence alignment space
-
Contreras-Moreira B, Fitzjohn PW, Offman M, Smith GR, Bates PA. Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins 2003;53(Suppl 6):424-429.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 424-429
-
-
Contreras-Moreira, B.1
Fitzjohn, P.W.2
Offman, M.3
Smith, G.R.4
Bates, P.A.5
-
15
-
-
23144465987
-
-
Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005;33(Web Server Issue):W72-W76.
-
Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005;33(Web Server Issue):W72-W76.
-
-
-
-
16
-
-
30344438515
-
Automated prediction of domain boundaries in CASP6 targets using Ginzu and Rosetta-DOM
-
Kim DE, Chivian D, Malmstrom L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and Rosetta-DOM. Proteins 2005;61(Suppl 7):193-200.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 193-200
-
-
Kim, D.E.1
Chivian, D.2
Malmstrom, L.3
Baker, D.4
-
17
-
-
84860507958
-
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
-
Cheng J, Baldi P. Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005;21(Suppl 1):i75-i84.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Cheng, J.1
Baldi, P.2
-
18
-
-
14944345295
-
Development of an ab initio protein structure prediction system ABLE
-
Ishida T, Nishimura T, Nozaki M, Inoue T, Terada T, Nakamura S, Shimizu K. Development of an ab initio protein structure prediction system ABLE. Genome Inform 2003;14:228-237.
-
(2003)
Genome Inform
, vol.14
, pp. 228-237
-
-
Ishida, T.1
Nishimura, T.2
Nozaki, M.3
Inoue, T.4
Terada, T.5
Nakamura, S.6
Shimizu, K.7
-
19
-
-
33746952996
-
Protein disorder prediction by condensed PSSM considering propensity for order or disorder
-
Su CT, Chen CY, Ou YY. Protein disorder prediction by condensed PSSM considering propensity for order or disorder. BMC Bioinformatics 2006;7:319.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 319
-
-
Su, C.T.1
Chen, C.Y.2
Ou, Y.Y.3
-
20
-
-
11144220725
-
CPHmodels 2.0: X3M a Computer Program to Extract 3D Models
-
December, Asilomar, CA
-
Lund O, Nielsen M, Lundegaard C, Worning P. CPHmodels 2.0: X3M a Computer Program to Extract 3D Models. In: CASP5: Proceedings of the 5th meeting on the critical assessment of techniques for protein structure prediction, 1-5 December 2002, Asilomar, CA.
-
(2002)
CASP5: Proceedings of the 5th meeting on the critical assessment of techniques for protein structure prediction, 1-5
-
-
Lund, O.1
Nielsen, M.2
Lundegaard, C.3
Worning, P.4
-
21
-
-
3242891318
-
The DISOPRED server for the prediction of protein disorder
-
Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics 2004;20:2138-2139.
-
(2004)
Bioinformatics
, vol.20
, pp. 2138-2139
-
-
Ward, J.J.1
McGuffin, L.J.2
Bryson, K.3
Buxton, B.F.4
Jones, D.T.5
-
22
-
-
27944488680
-
Accurate prediction of protein disordered regions by mining protein structure data
-
Cheng J, Sweredoski MJ, Baldi P. Accurate prediction of protein disordered regions by mining protein structure data. Data Min Knowledge Discov 2005;11:213-222.
-
(2005)
Data Min Knowledge Discov
, vol.11
, pp. 213-222
-
-
Cheng, J.1
Sweredoski, M.J.2
Baldi, P.3
-
23
-
-
33749139123
-
Distill: A suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
-
Bau D, Martin AJ, Mooney C, Vullo A, Walsh I, Pollastri G. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. BMC Bioinformatics 2006;7:402.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 402
-
-
Bau, D.1
Martin, A.J.2
Mooney, C.3
Vullo, A.4
Walsh, I.5
Pollastri, G.6
-
24
-
-
34247566179
-
Computer-assisted protein domain boundary prediction using the DomPred server
-
Bryson K, Cozzetto D, Jones DT. Computer-assisted protein domain boundary prediction using the DomPred server. Curr Protein Pept Sci 2007;8:181-188.
-
(2007)
Curr Protein Pept Sci
, vol.8
, pp. 181-188
-
-
Bryson, K.1
Cozzetto, D.2
Jones, D.T.3
-
25
-
-
0034465184
-
An automatic homology modeling method consisting of database searches and simulated annealing
-
Ogata K, Umeyama H. An automatic homology modeling method consisting of database searches and simulated annealing. J Mol Graph Model 2000;18:258-272, 305-256.
-
(2000)
J Mol Graph Model
, vol.18
-
-
Ogata, K.1
Umeyama, H.2
-
26
-
-
33745616114
-
A machine learning information retrieval approach to protein fold recognition
-
Cheng J, Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006;22:1456-1463.
-
(2006)
Bioinformatics
, vol.22
, pp. 1456-1463
-
-
Cheng, J.1
Baldi, P.2
-
27
-
-
1542609543
-
FORTE: A profile-profile comparison tool for protein fold recognition
-
Tomii K, Akiyama Y. FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics 2004;20:594-595.
-
(2004)
Bioinformatics
, vol.20
, pp. 594-595
-
-
Tomii, K.1
Akiyama, Y.2
-
28
-
-
30344463291
-
Protein structure prediction using a variety of profile libraries and 3D verification
-
Tomii K, Hirokawa T, Motono C. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 2005;61 (Suppl 7):114-121.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 114-121
-
-
Tomii, K.1
Hirokawa, T.2
Motono, C.3
-
29
-
-
30344466041
-
FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6
-
Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. Proteins 2005;61(Suppl 7):106-113.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 106-113
-
-
Kosinski, J.1
Gajda, M.J.2
Cymerman, I.A.3
Kurowski, M.A.4
Pawlowski, M.5
Boniecki, M.6
Obarska, A.7
Papaj, G.8
Sroczynska-Obuchowicz, P.9
Tkaczuk, K.L.10
Sniezynska, P.11
Sasin, J.M.12
Augustyn, A.13
Bujnicki, J.M.14
Feder, M.15
-
30
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310:243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
31
-
-
0043123216
-
GeneSilico protein structure prediction meta-server
-
Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003;31:3305-3307.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3305-3307
-
-
Kurowski, M.A.1
Bujnicki, J.M.2
-
32
-
-
24744453057
-
Striped sheets and protein contact prediction
-
MacCallum RM. Striped sheets and protein contact prediction. Bioinformatics 2004;20(Suppl 1):I224-I231.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
MacCallum, R.M.1
-
33
-
-
23144452044
-
-
Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33(Web Server Issue):W244-W248.
-
Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005;33(Web Server Issue):W244-W248.
-
-
-
-
34
-
-
3242889054
-
-
Torda AE, Procter JB, Huber T. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res 2004;32 (Web Server Issue):W532-W535.
-
Torda AE, Procter JB, Huber T. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res 2004;32 (Web Server Issue):W532-W535.
-
-
-
-
35
-
-
28444492998
-
Profile-based direct kernels for remote homology detection and fold recognition
-
Rangwala H, Karypis G. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics 2005;21:4239-4247.
-
(2005)
Bioinformatics
, vol.21
, pp. 4239-4247
-
-
Rangwala, H.1
Karypis, G.2
-
36
-
-
33750948399
-
Building multiclass classifiers for remote homology detection and fold recognition
-
Rangwala H, Karypis G. Building multiclass classifiers for remote homology detection and fold recognition. BMC Bioinformatics 2006;7:455.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 455
-
-
Rangwala, H.1
Karypis, G.2
-
37
-
-
27544480322
-
MESHI: A new library of Java classes for molecular modeling
-
Kalisman N, Levi A, Maximova T, Reshef D, Zafriri-Lynn S, Gleyzer Y, Keasar C. MESHI: a new library of Java classes for molecular modeling. Bioinformatics 2005;21:3931-3932.
-
(2005)
Bioinformatics
, vol.21
, pp. 3931-3932
-
-
Kalisman, N.1
Levi, A.2
Maximova, T.3
Reshef, D.4
Zafriri-Lynn, S.5
Gleyzer, Y.6
Keasar, C.7
-
38
-
-
0035889689
-
Linear programming optimization and a double statistical filter for protein threading protocols
-
Meller J, Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins 2001;45:241-261.
-
(2001)
Proteins
, vol.45
, pp. 241-261
-
-
Meller, J.1
Elber, R.2
-
39
-
-
0348047626
-
Enriching the sequence substitution matrix by structural information
-
Teodorescu O, Galor T, Pillardy J, Elber R. Enriching the sequence substitution matrix by structural information. Proteins 2004;54:41-48.
-
(2004)
Proteins
, vol.54
, pp. 41-48
-
-
Teodorescu, O.1
Galor, T.2
Pillardy, J.3
Elber, R.4
-
40
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: Results from linear optimization
-
Tobi D, Elber R. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins 2000;41:40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
41
-
-
20844435796
-
Meta-DP: Domain prediction meta-server
-
Saini HK, Fischer D. Meta-DP: domain prediction meta-server. Bioinformatics 2005;21:2917-2920.
-
(2005)
Bioinformatics
, vol.21
, pp. 2917-2920
-
-
Saini, H.K.1
Fischer, D.2
-
42
-
-
33845365051
-
TASSER-Lite: An automated tool for protein comparative modeling
-
Pandit SB, Zhang Y, Skolnick J. TASSER-Lite: an automated tool for protein comparative modeling. Biophys J 2006;91:4180-4190.
-
(2006)
Biophys J
, vol.91
, pp. 4180-4190
-
-
Pandit, S.B.1
Zhang, Y.2
Skolnick, J.3
-
43
-
-
2442676589
-
Automated structure prediction of weakly homologous proteins on a genomic scale
-
Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
44
-
-
36749095600
-
Analysis of TASSER based CASP7 protein structure prediction results
-
Zhou H, Pandit SB, Lee SY, Borreguero J, Chen H, Wroblewska L, Skolnick J. Analysis of TASSER based CASP7 protein structure prediction results. Proteins 2007;69(Suppl 8):90-97.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 90-97
-
-
Zhou, H.1
Pandit, S.B.2
Lee, S.Y.3
Borreguero, J.4
Chen, H.5
Wroblewska, L.6
Skolnick, J.7
-
45
-
-
30344442116
-
Prediction of novel and analogous folds using fragment assembly and fold recognition
-
Jones DT, Bryson K, Coleman A, McGuffin LJ, Sadowski MI, Sodhi JS, Ward JJ. Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins 2005;61 (Suppl 7):143-151.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 143-151
-
-
Jones, D.T.1
Bryson, K.2
Coleman, A.3
McGuffin, L.J.4
Sadowski, M.I.5
Sodhi, J.S.6
Ward, J.J.7
-
46
-
-
34547612652
-
Pcons.net: Protein structure prediction meta server. Nucleic Acids Res
-
Web Server Issue:W369-W374
-
Wallner B, Larsson P, Elofsson A. Pcons.net: protein structure prediction meta server. Nucleic Acids Res 2007;35 (Web Server Issue):W369-W374.
-
(2007)
, pp. 35
-
-
Wallner, B.1
Larsson, P.2
Elofsson, A.3
-
47
-
-
33744471931
-
Enhanced automated function prediction using distantly related sequences and contextual association by PFP
-
Hawkins T, Luban S, Kihara D. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci 2006;15:1550-1556.
-
(2006)
Protein Sci
, vol.15
, pp. 1550-1556
-
-
Hawkins, T.1
Luban, S.2
Kihara, D.3
-
48
-
-
4043170491
-
Protein contact prediction using patterns of correlation
-
Hamilton N, Burrage K, Ragan MA, Huber T. Protein contact prediction using patterns of correlation. Proteins 2004;56:679-684.
-
(2004)
Proteins
, vol.56
, pp. 679-684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.A.3
Huber, T.4
-
49
-
-
21444454088
-
PROFcon: Novel prediction of long-range contacts
-
Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics 2005;21:2960-2968.
-
(2005)
Bioinformatics
, vol.21
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
50
-
-
21444448763
-
-
Hung LH, Ngan SC, Liu T, Samudrala R. PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res 2005;33(Web Server Issue):W77-W80.
-
Hung LH, Ngan SC, Liu T, Samudrala R. PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res 2005;33(Web Server Issue):W77-W80.
-
-
-
-
52
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003;1:95-117.
-
(2003)
J Bioinform Comput Biol
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
53
-
-
36749056780
-
Consensus approaches for protein structure prediction
-
Zhang YQ, Jagath CR, editors, New York: Wiley;
-
Bu D, Li S, Gao X, Yu L, Xu J, Li M. Consensus approaches for protein structure prediction. In: Zhang YQ, Jagath CR, editors. Machine Learning in Bioinformatics. New York: Wiley; 2007.
-
(2007)
Machine Learning in Bioinformatics
-
-
Bu, D.1
Li, S.2
Gao, X.3
Yu, L.4
Xu, J.5
Li, M.6
-
54
-
-
10744230917
-
Automated prediction of CASP-5 structures using the Roberta server
-
Chivian D, Kim DE, Malmstrom L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Roberta server. Proteins 2003;53 (Suppl 6):524-533.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 524-533
-
-
Chivian, D.1
Kim, D.E.2
Malmstrom, L.3
Bradley, P.4
Robertson, T.5
Murphy, P.6
Strauss, C.E.7
Bonneau, R.8
Rohl, C.A.9
Baker, D.10
-
55
-
-
24344503079
-
Protein flexibility and rigidity predicted from sequence
-
Schlessinger A, Rost B. Protein flexibility and rigidity predicted from sequence. Proteins 2005;61:115-126.
-
(2005)
Proteins
, vol.61
, pp. 115-126
-
-
Schlessinger, A.1
Rost, B.2
-
56
-
-
33645288849
-
PROFbval: Predict flexible and rigid residues in proteins
-
Schlessinger A, Yachdav G, Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 2006;22:891-893.
-
(2006)
Bioinformatics
, vol.22
, pp. 891-893
-
-
Schlessinger, A.1
Yachdav, G.2
Rost, B.3
-
57
-
-
30344452280
-
SAM-T04: What is new in protein-structure prediction for CASP6
-
Karplus K, Katzman S, Shackleford G, Koeva M, Draper J, Barnes B, Soriano M, Hughey R. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 2005;61(Suppl 7):135-142.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 135-142
-
-
Karplus, K.1
Katzman, S.2
Shackleford, G.3
Koeva, M.4
Draper, J.5
Barnes, B.6
Soriano, M.7
Hughey, R.8
-
58
-
-
0242362161
-
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
-
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003;53(Suppl 6):491-496.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Draper, J.3
Casper, J.4
Mandel-Gutfreund, Y.5
Diekhans, M.6
Hughey, R.7
-
59
-
-
0032613203
-
Predicting protein structure using only sequence information
-
Karplus K, Barrett C, Cline M, Diekhans M, Grate L, Hughey R. Predicting protein structure using only sequence information. Proteins 1999;37(Suppl 3):121-125.
-
(1999)
Proteins
, vol.37
, Issue.SUPPL. 3
, pp. 121-125
-
-
Karplus, K.1
Barrett, C.2
Cline, M.3
Diekhans, M.4
Grate, L.5
Hughey, R.6
-
60
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005;58:321-328.
-
(2005)
Proteins
, vol.58
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
-
61
-
-
34447506573
-
Fold Recognition by concurrent use of solvent accessibility and residue depth
-
Liu S, Zhang C, Liang S, Zhou Y. Fold Recognition by concurrent use of solvent accessibility and residue depth. Proteins 2007;68:636-645.
-
(2007)
Proteins
, vol.68
, pp. 636-645
-
-
Liu, S.1
Zhang, C.2
Liang, S.3
Zhou, Y.4
-
62
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007;8:113.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
63
-
-
20844438702
-
Convergent island statistics: A fast method for determining local alignment score significance
-
Poleksic A, Danzer JF, Hambly K, Debe DA. Convergent island statistics: a fast method for determining local alignment score significance. Bioinformatics 2005;21:2827-2831.
-
(2005)
Bioinformatics
, vol.21
, pp. 2827-2831
-
-
Poleksic, A.1
Danzer, J.F.2
Hambly, K.3
Debe, D.A.4
-
64
-
-
33748449489
-
STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring
-
Debe DA, Danzer JF, Goddard WA, Poleksic A. STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring. Proteins 2006;64:960-967.
-
(2006)
Proteins
, vol.64
, pp. 960-967
-
-
Debe, D.A.1
Danzer, J.F.2
Goddard, W.A.3
Poleksic, A.4
-
65
-
-
36749061828
-
Template-based modeling and free modeling by I-TASSER in CASP7
-
Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007;69(Suppl 8):108-117.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 108-117
-
-
Zhang, Y.1
-
66
-
-
36749086922
-
Assessment of CASP7 structure predictions for template free targets
-
Jauch R, Yeo H, Kolatkar PR, Clarke ND. Assessment of CASP7 structure predictions for template free targets. Proteins 2007;69 (Suppl 8):57-67.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 57-67
-
-
Jauch, R.1
Yeo, H.2
Kolatkar, P.R.3
Clarke, N.D.4
-
67
-
-
36749099341
-
Assessment of CASP7 predictions for template-based modeling targets
-
Kopp J, Bordoli L, Battey JND, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007;69(Suppl 8):38-56.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 38-56
-
-
Kopp, J.1
Bordoli, L.2
Battey, J.N.D.3
Kiefer, F.4
Schwede, T.5
-
68
-
-
36749059956
-
Assessment of CASP7 predictions in the high accuracy template-based modeling category
-
Read RJ, Chavali G. Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 2007;69 (Suppl 8):27-37.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 27-37
-
-
Read, R.J.1
Chavali, G.2
-
69
-
-
36749081458
-
Assessment of disorder predictions in CASP7
-
Bordoli L, Kiefer F, Schwede T. Assessment of disorder predictions in CASP7. Proteins 2007;69(Suppl 8):129-136.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 129-136
-
-
Bordoli, L.1
Kiefer, F.2
Schwede, T.3
-
70
-
-
36749014942
-
Assessment of predictions submitted for the CASP7 domain prediction category
-
Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo J-H, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins 2007;69(Suppl 8):137-151.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 137-151
-
-
Tress, M.1
Cheng, J.2
Baldi, P.3
Joo, K.4
Lee, J.5
Seo, J.-H.6
Lee, J.7
Baker, D.8
Chivian, D.9
Kim, D.10
Ezkurdia, I.11
-
71
-
-
36749082814
-
Assessment of intramolecular contact predictions for CASP7
-
Izarzugaza JMG, Graña O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins 2007;69(Suppl 8):152-158.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 152-158
-
-
Izarzugaza, J.M.G.1
Graña, O.2
Tress, M.L.3
Valencia, A.4
Clarke, N.D.5
-
72
-
-
36748998785
-
Assessment of predictions submitted for the CASP7 function prediction category
-
López G, Rajas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins 2007;69(Suppl 8):165-174.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 165-174
-
-
López, G.1
Rajas, A.2
Tress, M.3
Valencia, A.4
-
73
-
-
33846033844
-
-
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 2007;35 (Database Issue): D291-D297.
-
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 2007;35 (Database Issue): D291-D297.
-
-
-
-
74
-
-
36749050816
-
Domain definition and target classification for CASP7
-
Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M. Domain definition and target classification for CASP7. Proteins 2007;69(Suppl 8):10-18.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 10-18
-
-
Clarke, N.D.1
Ezkurdia, I.2
Kopp, J.3
Read, R.J.4
Schwede, T.5
Tress, M.6
-
75
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
76
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
77
-
-
33846062023
-
-
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007;35 (Database Issue):D5-D12.
-
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2007;35 (Database Issue):D5-D12.
-
-
-
-
78
-
-
0031302732
-
Assessment of comparative modeling in CASP2
-
Martin AC, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins 1997;29(Suppl 1):14-28.
-
(1997)
Proteins
, vol.29
, Issue.SUPPL. 1
, pp. 14-28
-
-
Martin, A.C.1
MacArthur, M.W.2
Thornton, J.M.3
-
79
-
-
0030053370
-
ProMod and Swiss-model: Internet-based tools for automated comparative protein modelling
-
Peitsch MC. ProMod and Swiss-model: internet-based tools for automated comparative protein modelling. Biochem Soc Trans 1996;24:274-279.
-
(1996)
Biochem Soc Trans
, vol.24
, pp. 274-279
-
-
Peitsch, M.C.1
-
80
-
-
11144241105
-
LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
-
Rychlewski L, Fischer D. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci 2005;14:240-245.
-
(2005)
Protein Sci
, vol.14
, pp. 240-245
-
-
Rychlewski, L.1
Fischer, D.2
-
81
-
-
0043123211
-
EVA: Evaluation of protein structure prediction servers
-
Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, Rost B. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 2003;31:3311-3315.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3311-3315
-
-
Koh, I.Y.1
Eyrich, V.A.2
Marti-Renom, M.A.3
Przybylski, D.4
Madhusudhan, M.S.5
Eswar, N.6
Grana, O.7
Pazos, F.8
Valencia, A.9
Sali, A.10
Rost, B.11
|