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Volumn 10, Issue SUPPL. 1, 2010, Pages

Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; GENETIC ALGORITHM; INFORMATION PROCESSING; MACHINE LEARNING; RANDOM SAMPLE; SEQUENCE ANALYSIS; SUPPORT VECTOR MACHINE; ALGORITHM; ARTIFICIAL INTELLIGENCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 77952597524     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-10-S1-S2     Document Type: Article
Times cited : (22)

References (43)
  • 1
    • 0034635337 scopus 로고    scopus 로고
    • Exploring local and non-local interactions for protein stability by structural motif engineering
    • 10656826
    • Exploring local and non-local interactions for protein stability by structural motif engineering. M Niggemann B Steipe, J Mol Biol 2000 296 181 195 10656826
    • (2000) J Mol Biol , vol.296 , pp. 181-195
    • Niggemann, M.1    Steipe, B.2
  • 3
    • 0033047710 scopus 로고    scopus 로고
    • A neural network based predictor of residue contacts in proteins
    • 10065706
    • A neural network based predictor of residue contacts in proteins. P Fariselli R Casadio, Protein Engineering 1999 12 15 21 10065706
    • (1999) Protein Engineering , vol.12 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 4
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • 9377713
    • Recovery of protein structure from contact maps. M Vendruscolo E Kussell E Domany, Fold Des 1997 2 295 306 9377713
    • (1997) Fold des , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Kussell, E.2    Domany, E.3
  • 5
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    • 12169532
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. G Pollastri P Baldi, Bioinformatics 2002 18 62 S70 12169532
    • (2002) Bioinformatics , vol.18
    • Pollastri, G.1    Baldi, P.2
  • 6
    • 13944252115 scopus 로고    scopus 로고
    • Prediction of distant residue contacts with the use of evolutionary information
    • 15645442
    • Prediction of distant residue contacts with the use of evolutionary information. S Vicatos VBR Boojala Y Kaznessis, Proteins 2005 58 935 949 15645442
    • (2005) Proteins , vol.58 , pp. 935-949
    • Vicatos, S.1    Boojala, V.B.R.2    Kaznessis, Y.3
  • 7
    • 24744453057 scopus 로고    scopus 로고
    • Striped sheets and protein contact prediction
    • 15262803
    • Striped sheets and protein contact prediction. RM MacCallum, Bioinformatics 2004 20 Suppl 1 224 i231 15262803
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL 1
    • MacCallum, R.M.1
  • 8
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • 11742102
    • Prediction of contact maps with neural networks and correlated mutations. P Fariselli O Olmea A Valencia R Casadio, Protein Engineering 2001 14 835 843 11742102
    • (2001) Protein Engineering , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 9
    • 43749113791 scopus 로고    scopus 로고
    • Predicting contact map using radial basis function neural network with conformational energy function
    • 18490258
    • Predicting Contact Map Using Radial Basis Function Neural Network with Conformational Energy Function. P Chen DS Huang XM Zhao X Li, Int J Bioinform Res Appl 2008 4 123 136 18490258
    • (2008) Int J Bioinform Res Appl , vol.4 , pp. 123-136
    • Chen, P.1    Huang, D.S.2    Zhao, X.M.3    Li, X.4
  • 10
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • 17407573
    • Improved residue contact prediction using support vector machines and a large feature set. J Cheng P Baldi, BMC Bioinformatics 2007 8 113 17407573
    • (2007) BMC Bioinformatics , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 11
    • 45749134979 scopus 로고    scopus 로고
    • Predicting key long-range interaction sites by b-factors
    • 18537737
    • Predicting Key Long-Range Interaction Sites by B-Factors. P Chen K Han X Li DS Huang, Protein Pept Lett 2008 15 5 478 483 18537737
    • (2008) Protein Pept Lett , vol.15 , Issue.5 , pp. 478-483
    • Chen, P.1    Han, K.2    Li, X.3    Huang, D.S.4
  • 12
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel prediction of long-range contacts
    • 15890748
    • PROFcon: novel prediction of long-range contacts. M Punta B Rost, Bioinformatics 2005 21 2960 2968 15890748
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 13
    • 33745610096 scopus 로고    scopus 로고
    • A two-stage approach for improved prediction of residue contact maps
    • 16573808
    • A two-stage approach for improved prediction of residue contact maps. A Vullo L Walsh G Pollastri, BMC Bioinformatics 2006 7 180 16573808
    • (2006) BMC Bioinformatics , vol.7 , pp. 180
    • Vullo, A.1    Walsh, L.2    Pollastri, G.3
  • 14
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • 18296462
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. S Wu Y Zhang, Bioinformatics 2008 24 924 931 18296462
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 15
    • 67849110005 scopus 로고    scopus 로고
    • NNcon: Improved protein contact map prediction using 2D-recursive neural networks
    • 19420062
    • NNcon: improved protein contact map prediction using 2D-recursive neural networks. AN Tegge Z Wang J Eickholt J Cheng, Nucleic Acids Research 2009 37 515 W518 19420062
    • (2009) Nucleic Acids Research , vol.37
    • Tegge, A.N.1    Wang, Z.2    Eickholt, J.3    Cheng, J.4
  • 17
    • 0031406438 scopus 로고    scopus 로고
    • Protein distance constraints predicted by neural networks and probability density functions
    • 9514112
    • Protein distance constraints predicted by neural networks and probability density functions. O Lund K Frimand J Gorodkin H Bohr J Bohr J Hansen S Brunak, Protein Eng 1997 10 1241 1248 9514112
    • (1997) Protein Eng , vol.10 , pp. 1241-1248
    • Lund, O.1    Frimand, K.2    Gorodkin, J.3    Bohr, H.4    Bohr, J.5    Hansen, J.6    Brunak, S.7
  • 19
    • 0029097099 scopus 로고
    • Global Fold Determination from a Small Number of Distance Restraints
    • 7643405
    • Global Fold Determination from a Small Number of Distance Restraints. A Aszodi MJ Gradwell WR Taylor, Journal of Molecular Biology 1995 251 2 308 326 7643405
    • (1995) Journal of Molecular Biology , vol.251 , Issue.2 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 20
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scal
    • 15126668
    • Automated structure prediction of weakly homologous proteins on a genomic scal. Y Zhang J Skolnick, PNAS 2004 101 7594 7599 15126668
    • (2004) PNAS , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 21
    • 0031575423 scopus 로고    scopus 로고
    • MONSTER: A method for folding globular Proteins with a small number of distance restraints
    • 9020984
    • MONSTER: A method for folding globular Proteins with a small number of distance restraints. J Skolnick A Kolinski A Ortiz, J Mol Biol 1997 265 217 241 9020984
    • (1997) J Mol Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.3
  • 22
    • 0032613288 scopus 로고    scopus 로고
    • Ab initio folding of proteins using restraints derived from evolutionary information
    • 10526366
    • Ab initio folding of proteins using restraints derived from evolutionary information. AR Ortiz A Kolinski P Rotkiewicz B Ilkowski J Skolnick, Proteins 1999 Suppl 3 177 185 10526366
    • (1999) Proteins , vol.3 , pp. 177-185
    • Ortiz, A.R.1    Kolinski, A.2    Rotkiewicz, P.3    Ilkowski, B.4    Skolnick, J.5
  • 23
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • TOUCHSTONE II: a new approach to ab initio protein structure prediction. Y Zhang A Kolinski J Skolnick, Biophysical Journal 2003 85 1145 1164 12885659 (Pubitemid 36909676)
    • (2003) Biophysical Journal , vol.85 , Issue.2 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 25
    • 30344459116 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP) - Round VI
    • 16187341
    • Critical assessment of methods of protein structure prediction (CASP) - round VI. J Moult K Fidelis A Tramontano B Rost T Hubbard, Proteins 2005 61 3 7 16187341
    • (2005) Proteins , vol.61 , pp. 3-7
    • Moult, J.1    Fidelis, K.2    Tramontano, A.3    Rost, B.4    Hubbard, T.5
  • 26
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and interresidue contacts
    • 11835487
    • Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. A Lesk LL Conte T Hubbard, Proteins 2001 Suppl 5 98 118 11835487
    • (2001) Proteins , vol.5 , pp. 98-118
    • Lesk, A.1    Conte, L.L.2    Hubbard, T.3
  • 29
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein beta-sheets by neural networks, alignments, and graph algorithms
    • 15961501
    • Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms. J Cheng P Baldi, Bioinformatics 2005 21 75 i84 15961501
    • (2005) Bioinformatics , vol.21
    • Cheng, J.1    Baldi, P.2
  • 30
    • 33749139123 scopus 로고    scopus 로고
    • Distill: A suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins
    • 16953874
    • Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins. D Bau AJ Martin C Mooney A Vullo I Walsh G Pollastri, BMC Bioinformatics 2006 7 402 16953874
    • (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
  • 31
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using patterns of correlation
    • 15281121
    • Protein contact prediction using patterns of correlation. N Hamilton K Burrage M Ragan T Huber, Proteins 2004 56 679 684 15281121
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.3    Huber, T.4
  • 32
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • 9927713
    • Hidden Markov models for detecting remote protein homologies. K Karplus C Barrett R Hughey, Bioinformatics 1998 14 846 856 9927713
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 34
    • 0037250308 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
    • 12520060
    • PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. T Noguchi Y Akiyama, Nucleic Acids Res 2003 31 492 493 12520060
    • (2003) Nucleic Acids Res , vol.31 , pp. 492-493
    • Noguchi, T.1    Akiyama, Y.2
  • 35
    • 12944257228 scopus 로고    scopus 로고
    • The ConSurf-HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures
    • 15614759
    • The ConSurf-HSSP Database: The Mapping of Evolutionary Conservation Among Homologs Onto PDB Structures. F Glaser Y Rosenberg A Kessel T Pupko N Ben-Tal, Proteins 2005 58 610 617 15614759
    • (2005) Proteins , vol.58 , pp. 610-617
    • Glaser, F.1    Rosenberg, Y.2    Kessel, A.3    Pupko, T.4    Ben-Tal, N.5
  • 37
    • 0031841279 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments and family profiles
    • 9399862
    • The HSSP database of protein structure-sequence alignments and family profiles. C Dodge R Schneider C Sander, Nucleic Acids Res 1998 26 313 315 9399862
    • (1998) Nucleic Acids Res , vol.26 , pp. 313-315
    • Dodge, C.1    Schneider, R.2    Sander, C.3
  • 38
    • 0346688667 scopus 로고    scopus 로고
    • An optimal structure-discriminative amino acid index for protein fold recognition
    • 14695283
    • An Optimal Structure-Discriminative Amino Acid Index for Protein Fold Recognition. RHJ Leary B Rosen P Jambeckz, Biophysical Journal 2004 86 411 419 14695283
    • (2004) Biophysical Journal , vol.86 , pp. 411-419
    • Leary, R.H.J.1    Rosen, B.2    Jambeckz, P.3
  • 43
    • 0242299155 scopus 로고    scopus 로고
    • CAFASP3: The third critical assessment of fully automated structure prediction methods
    • 14579340
    • CAFASP3: the third critical assessment of fully automated structure prediction methods. D Fischer L Rychlewski RL Dunbrack AR Ortiz A Elofsson, Proteins 2003 53 Suppl 6 503 516 14579340
    • (2003) Proteins , vol.53 , Issue.SUPPL 6 , pp. 503-516
    • Fischer, D.1    Rychlewski, L.2    Dunbrack, R.L.3    Ortiz, A.R.4    Elofsson, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.