-
1
-
-
36749042541
-
Critical assessment of methods of protein structure prediction - Round VII
-
DOI 10.1002/prot.21767
-
Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A. Critical assessment of methods of protein structure prediction-round VII. Proteins 2007;69 (Suppl 8):3-9. (Pubitemid 350210108)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 3-9
-
-
Moult, J.1
Fidelis, K.2
Kryshtafovych, A.3
Rost, B.4
Hubbard, T.5
Tramontano, A.6
-
2
-
-
0030627407
-
Recovery of protein structure from contact maps
-
Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Fold Design 1997;2:295-306. (Pubitemid 127740552)
-
(1997)
Folding and Design
, vol.2
, Issue.5
, pp. 295-306
-
-
Vendruscolo, M.1
Kussell, E.2
Domany, E.3
-
3
-
-
0036073603
-
Contact order and ab initio protein structure prediction
-
Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Sci 2002;11:1937-1944.
-
(2002)
Protein Sci
, vol.11
, pp. 1937-1944
-
-
Bonneau, R.1
Ruczinski, I.2
Tsai, J.3
Baker, D.4
-
4
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
Goebel U, Sander C, Scheneider R, Valencia A. Correlated mutation and residue contacts in proteins. Proteins 1994;18:309-317. (Pubitemid 24111530)
-
(1994)
Proteins: Structure, Function and Genetics
, vol.18
, Issue.4
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
5
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Design 1997;2:s25-s32. (Pubitemid 127740476)
-
(1997)
Folding and Design
, vol.2
, Issue.3
-
-
Olmea, O.1
Valencia, A.2
-
6
-
-
4043170491
-
Protein contact prediction using patterns of correlation
-
DOI 10.1002/prot.20160
-
Hamilton N, Burrage K, Ragan M, Huber T. Protein contact prediction using patterns of correlation. Proteins 2004;56:679-684. (Pubitemid 39063311)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.4
, pp. 679-684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.A.3
Huber, T.4
-
7
-
-
33646766064
-
Correlated mutations: Advances and limitations. a study on fusion proteins and on the cohesion-dockerin families
-
Halperin I, Wolfson HJ, Nussinov R. Correlated mutations: advances and limitations. A study on fusion proteins and on the cohesion-dockerin families. Proteins 2006;63:832-845.
-
(2006)
Proteins
, vol.63
, pp. 832-845
-
-
Halperin, I.1
Wolfson, H.J.2
Nussinov, R.3
-
8
-
-
33751219893
-
Predicting residue contacts using pragmatic correlated mutations method: Reducing the false positives
-
Kundrotas PJ, Alexov EG. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinformatics 2006;7:503.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 503
-
-
Kundrotas, P.J.1
Alexov, E.G.2
-
9
-
-
0033047710
-
A neural network based predictor of residue contacts in proteins
-
Fariselli P, Casadio R. A neural network based predictor of residue contacts in proteins. Prot Eng 1999;12:15-21. (Pubitemid 29050537)
-
(1999)
Protein Engineering
, vol.12
, Issue.1
, pp. 15-21
-
-
Fariselli, P.1
Casadio, R.2
-
10
-
-
0035700864
-
Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations
-
DOI 10.1002/prot.1173
-
Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins 2001;(Suppl 5):157-162. (Pubitemid 34113179)
-
(2001)
Proteins: Structure, Function and Genetics
, vol.45
, Issue.SUPPL. 5
, pp. 157-162
-
-
Fariselli, P.1
Olmea, O.2
Valencia, A.3
Casadio, R.4
-
11
-
-
0035237804
-
Improved prediction of the number of residue contacts in proteins by recurrent neural networks
-
Pollastri G, Baldi P, Fariselli P, Casadio R. Improved prediction of the number of residue contacts in proteins by recurrent neural networks. 4Bioinformatics 2001;17:s234-s242. (Pubitemid 33793515)
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pollastri, G.1
Baldi, P.2
Fariselli, P.3
Casadio, R.4
-
12
-
-
0041719954
-
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
-
Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 2002;18:s62-s70. (Pubitemid 41185638)
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Pollastri, G.1
Baldi, P.2
-
13
-
-
22144489879
-
Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme
-
DOI 10.1007/s10822-005-0578-7
-
Zhang G, Huang DS. Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J Comput-Aided Mol Des 2004;18:797-810. (Pubitemid 40973868)
-
(2004)
Journal of Computer-Aided Molecular Design
, vol.18
, Issue.12
, pp. 797-810
-
-
Zhang, G.-Z.1
Huang, D.-S.2
-
14
-
-
21444454088
-
PROFcon: Novel prediction of long-range contacts
-
DOI 10.1093/bioinformatics/bti454
-
Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics 2005;21:2960-2968. (Pubitemid 40916420)
-
(2005)
Bioinformatics
, vol.21
, Issue.13
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
15
-
-
33745610096
-
A two-stage approach from improved prediction of residue contact maps
-
Vullo IA, Walsh , Pollastri G. A two-stage approach from improved prediction of residue contact maps. BMC Bioinformatics 2006;7:180.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 180
-
-
Vullo, I.A.1
Walsh2
Pollastri, G.3
-
17
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
DOI 10.1186/1471-2105-8-113
-
Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007;8:113. (Pubitemid 46605894)
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
18
-
-
0042721397
-
Predicting Interresidue Contacts Using Templates and Pathways
-
DOI 10.1002/prot.10539
-
Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins 2003;53:497-502. (Pubitemid 37352209)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.SUPPL. 6
, pp. 497-502
-
-
Shao, Y.1
Bystroff, C.2
-
19
-
-
24744453057
-
Striped sheets and protein contact prediction
-
Maccallum RM. Striped sheets and protein contact prediction. Bioinformatics 2004;20:224-231.
-
(2004)
Bioinformatics
, vol.20
, pp. 224-231
-
-
Maccallum, R.M.1
-
20
-
-
16344377463
-
Evolution and similarity evaluation of protein structures in contact map space
-
DOI 10.1002/prot.20415
-
Gupta NN, Mangal, Biswas S. Evolution and similarity evaluation of protein structures in contact map space. Proteins 2005;59:196-204. (Pubitemid 40471559)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.2
, pp. 196-204
-
-
Gupta, N.1
Mangal, N.2
Biswas, S.3
-
21
-
-
36749082814
-
Assessment of intramolecular contact predictions for CASP7
-
DOI 10.1002/prot.21637
-
Izarzugaza J, Grana O, Tress M, Valencia A, Clarke N. Assessment of intermolecular contact prediction for CASP7. Proteins 2007;69(Suppl):152-158. (Pubitemid 350210122)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 152-158
-
-
Izarzugaza, J.M.G.1
Grana, O.2
Tress, M.L.3
Valencia, A.4
Clarke, N.D.5
-
22
-
-
47049101751
-
Using inferred residue contacts to distinguish between correct and incorrect protein models
-
Miller C, Eisenberg D. Using inferred residue contacts to distinguish between correct and incorrect protein models. Bioinformatics 2008;24:1575-1582.
-
(2008)
Bioinformatics
, vol.24
, pp. 1575-1582
-
-
Miller, C.1
Eisenberg, D.2
-
23
-
-
0041843696
-
TOUCHSTONE II: A new approach to ab initio protein structure prediction
-
Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003;85:1145-1164. (Pubitemid 36909676)
-
(2003)
Biophysical Journal
, vol.85
, Issue.2
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
-
24
-
-
33847073796
-
Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training
-
DOI 10.1002/prot.21298
-
Dor O, Zhou Y. Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins 2007;66:838-845. (Pubitemid 46273069)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.4
, pp. 838-845
-
-
Dor, O.1
Zhou, Y.2
-
25
-
-
34249914807
-
Real-SPINE: An integrated system of neural networks for real-value prediction of protein structural properties
-
DOI 10.1002/prot.21408
-
Dor O, Zhou Y. Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties. Proteins 2007;68:76-81. (Pubitemid 46871583)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.68
, Issue.1
, pp. 76-81
-
-
Dor, O.1
Zhou, Y.2
-
26
-
-
61449123967
-
Improving the accuracy of predicting real-value backbone torsion angles and residue solvent accessibility by guided learning through two-layer neural networks
-
in press. (Published Online: Aug 14 2008, 1:54PM; DOI: 10.1002/prot.22193)
-
Faraggi E, Xue B, Zhou Y. Improving the accuracy of predicting real-value backbone torsion angles and residue solvent accessibility by guided learning through two-layer neural networks. Proteins, in press. (Published Online: Aug 14 2008, 1:54PM; DOI: 10.1002/prot.22193)
-
Proteins
-
-
Faraggi, E.1
Xue, B.2
Zhou, Y.3
-
27
-
-
44949201613
-
Real-value prediction of backbone torsion angles
-
Xue B, Dor O, Faraggi E, Zhou Y. Real-value prediction of backbone torsion angles. Proteins 2008;72:427-433.
-
(2008)
Proteins
, vol.72
, pp. 427-433
-
-
Xue, B.1
Dor, O.2
Faraggi, E.3
Zhou, Y.4
-
28
-
-
21844524655
-
Introduction to artificial neural network (ANN) methods: What they are and how to use them
-
Zupan J. Introduction to artificial neural network (ANN) methods: what they are and how to use them. Acta Chim Slovenica 1994;41:327-352.
-
(1994)
Acta Chim Slovenica
, vol.41
, pp. 327-352
-
-
Zupan, J.1
-
29
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul S, Madden T, Schaffer A, Zhang ZJ, Zhang, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Aci Res 1997;25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, 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
-
30
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
31
-
-
0029901640
-
Analysis of compositionally biased regions in sequence databases
-
DOI 10.1016/S0076-6879(96)66035-2
-
Wootton J, Federhen S. Analysis of compositionally biased regions in sequence databases. Meth Enzymol 1996;266:554-571. (Pubitemid 26165889)
-
(1996)
Methods in Enzymology
, vol.266
, pp. 554-571
-
-
Wootton, J.C.1
Federhen, S.2
-
32
-
-
2942694535
-
The dependence of all-atom statistical potentials on structural training database
-
DOI 10.1529/biophysj.103.035998
-
Zhang C, Liu S, Zhou H, Zhou Y. The dependence of all-atom statistical potentials on training structural database. Biophys J 2004;86:3349-3358. (Pubitemid 38780222)
-
(2004)
Biophysical Journal
, vol.86
, Issue.6
, pp. 3349-3358
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
33
-
-
0029984070
-
Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments
-
Riis S, Kroph A. Improving prediction of protein secondary structure using structured neural networks and multiple sequence alignments. J Comput Biol 1996;3:163-183. (Pubitemid 26182766)
-
(1996)
Journal of Computational Biology
, vol.3
, Issue.1
, pp. 163-183
-
-
Krogh, A.1
-
34
-
-
17844363963
-
PPRODO: Prediction of protein domain boundaries using neural networks
-
DOI 10.1002/prot.20442
-
Sim J, Kim S, Lee J. Pprodo: prediction of protein domain boundaries using neural networks. Proteins 2005;59:627-632. (Pubitemid 40594305)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.3
, pp. 627-632
-
-
Sim, J.1
Kim, S.-Y.2
Lee, J.3
-
35
-
-
84860164860
-
-
Available at: Accessed July 20, 2008
-
GraphPad Software. Available at: http://www.graphpad.com/quickcalcs/ ttest1.cfm. Accessed July 20, 2008.
-
-
-
-
36
-
-
84860507958
-
Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
-
DOI 10.1093/bioinformatics/bti1004
-
Cheng J, Baldi P. Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005;21(Suppl):i75-i84. (Pubitemid 41794477)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Cheng, J.1
Baldi, P.2
-
37
-
-
36749031067
-
Contact prediction using mutual information and neural nets
-
DOI 10.1002/prot.21791
-
Shackleford G, Karplus K. Contact prediction using mutual information and neural nets. Proteins 2007;69(S8):159-164. (Pubitemid 350210123)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 159-164
-
-
Shackelford, G.1
Karplus, K.2
|