메뉴 건너뛰기




Volumn 78, Issue 8, 2010, Pages 1980-1991

Predicted residue-residue contacts can help the scoring of 3D models

Author keywords

Protein structure; Residue residue contacts; Structural prediction

Indexed keywords

PROTEIN;

EID: 77953529848     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22714     Document Type: Article
Times cited : (29)

References (54)
  • 1
    • 0023660022 scopus 로고
    • Correlation of coordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh D, Lesk AM, Bloomer AC, Klug A. Correlation of coordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol. 1987; 193: 693-707.
    • (1987) J Mol Biol. , vol.193 , pp. 693-707
    • Altschuh, D.1    Lesk, A.M.2    Bloomer, A.C.3    Klug, A.4
  • 3
    • 0030627941 scopus 로고    scopus 로고
    • 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 Des Suppl 1997; 2: 25-32.
    • (1997) Fold des Suppl , vol.2 , pp. 25-32
    • Olmea, O.1    Valencia, A.2
  • 4
    • 33751219893 scopus 로고    scopus 로고
    • 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
  • 5
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • Fodor AA, Aldrich RW. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 2004; 56: 211-221.
    • (2004) Proteins , vol.56 , pp. 211-221
    • Fodor, A.A.1    Aldrich, R.W.2
  • 6
    • 0041719954 scopus 로고    scopus 로고
    • 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: 62-70.
    • (2002) Bioinformatics , vol.18 , pp. 62-70
    • Pollastri, G.1    Baldi, P.2
  • 7
    • 0042721397 scopus 로고    scopus 로고
    • Predicting interresidue contacts using templates and pathways
    • Shao Y, Bystroff C. Predicting interresidue contacts using templates and pathways. Proteins 2003; 53: 497-502.
    • (2003) Proteins , vol.53 , pp. 497-502
    • Shao, Y.1    Bystroff, C.2
  • 8
    • 24744453057 scopus 로고    scopus 로고
    • 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
  • 9
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel predictions of long-range contacts
    • Punta M, Rost B. PROFcon: novel predictions of long-range contacts. Bioinformatics 2005; 21: 2960-2968.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 10
    • 34247247779 scopus 로고    scopus 로고
    • 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
  • 11
    • 0035700864 scopus 로고    scopus 로고
    • Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations
    • Fariselli P, Olmea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins 2001; 5: 157-162.
    • (2001) Proteins , vol.5 , pp. 157-162
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 12
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • Shackelford G, Karplus K. Contact prediction using mutual information and neural nets. Proteins 2007; 69: 159-164.
    • (2007) Proteins , vol.69 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 13
    • 0031307080 scopus 로고    scopus 로고
    • CASP2: Report on ab initio predictions
    • Lesk AM. CASP2: report on ab initio predictions. Proteins 1997; 29: 151-166.
    • (1997) Proteins , vol.29 , pp. 151-166
    • Lesk, A.M.1
  • 14
    • 0032828469 scopus 로고    scopus 로고
    • Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    • Orengo CA, Bray JE, Hubbard TJP, LoConte L, Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins .1999; 37: 149-170.
    • (1999) Proteins , vol.37 , pp. 149-170
    • Orengo, C.A.1    Bray, J.E.2    Hubbard, T.J.P.3    LoConte, L.4    Sillitoe, I.5
  • 15
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and inter-residue contacts
    • Lesk AM, Lo Conte L, Hubbard TJP. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and inter-residue contacts. Proteins 2001; 45: 98-118.
    • (2001) Proteins , vol.45 , pp. 98-118
    • Lesk, A.M.1    Lo Conte, L.2    Hubbard, T.J.P.3
  • 16
    • 0242299187 scopus 로고    scopus 로고
    • Predictions without templates: New folds, secondary structure, and contacts in CASP5
    • Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins 2003; 53: 436-456.
    • (2003) Proteins , vol.53 , pp. 436-456
    • Aloy, P.1    Stark, A.2    Hadley, C.3    Russell, R.B.4
  • 19
    • 74249108517 scopus 로고    scopus 로고
    • Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
    • Ezkurdia I, Graña O, Izarzugaza JMG, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins 2009; 77: 196-209.
    • (2009) Proteins , vol.77 , pp. 196-209
    • Ezkurdia, I.1    Graña, O.2    Izarzugaza, J.M.G.3    Tress, M.L.4
  • 20
    • 59849106575 scopus 로고    scopus 로고
    • Optimal data collection for correlated mutation analysis
    • Ashkenazy H, Unger R, Kliger Y. Optimal data collection for correlated mutation analysis. Proteins 2009; 74: 545-555.
    • (2009) Proteins , vol.74 , pp. 545-555
    • Ashkenazy, H.1    Unger, R.2    Kliger, Y.3
  • 22
    • 65549127269 scopus 로고    scopus 로고
    • Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts
    • Björkholm P, Daniluk P, Kryshtafovych A, Fidelis K, Andersson R, Hvidsten TR. Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics 2009; 25: 1264-1270.
    • (2009) Bioinformatics , vol.25 , pp. 1264-1270
    • Björkholm, P.1    Daniluk, P.2    Kryshtafovych, A.3    Fidelis, K.4    Andersson, R.5    Hvidsten, T.R.6
  • 23
    • 61449104541 scopus 로고    scopus 로고
    • Towards accurate residueresidue hydrophobic contact prediction for alpha helical proteins via integer linear optimization
    • Rajgaria R, McAllister SR, Floudas CA. Towards accurate residueresidue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. Proteins 2009; 74: 929-947.
    • (2009) Proteins , vol.74 , pp. 929-947
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 24
    • 67849110005 scopus 로고    scopus 로고
    • NNcon: Improved protein contact map prediction using 2D-recursive neural networks
    • Tegge AN, Wang Z, Eickholt J, Cheng J. NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 2009; 37: W515-W518.
    • (2009) Nucleic Acids Res , vol.37
    • Tegge, A.N.1    Wang, Z.2    Eickholt, J.3    Cheng, J.4
  • 25
    • 61449126555 scopus 로고    scopus 로고
    • Ab initio and template-based prediction of multi-class distance maps by twodimensional recursive neural networks
    • Walsh I, Baù D, Martin AJ, Mooney C, Vullo A, Pollastri G. Ab initio and template-based prediction of multi-class distance maps by twodimensional recursive neural networks. BMC Struct Biol 2009; 9: 5.
    • (2009) BMC Struct Biol , vol.9 , pp. 5
    • Walsh, I.1    Baù, D.2    Martin, A.J.3    Mooney, C.4    Vullo, A.5    Pollastri, G.6
  • 26
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008; 24: 924-931.
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 27
    • 66249107719 scopus 로고    scopus 로고
    • Predicting residue-residue contact maps by a two-layer, integrated neural-network method
    • Xue B, Faraggi E, Zhou Y. Predicting residue-residue contact maps by a two-layer, integrated neural-network method. Proteins 2009; 76: 176-183.
    • (2009) Proteins , vol.76 , pp. 176-183
    • Xue, B.1    Faraggi, E.2    Zhou, Y.3
  • 28
    • 67849103757 scopus 로고    scopus 로고
    • SAM-T08, HMM-based protein structure prediction
    • Karplus K. SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res 2009; 37: W492-497.
    • (2009) Nucleic Acids Res , vol.37
    • Karplus, K.1
  • 29
    • 74249095557 scopus 로고    scopus 로고
    • Performance of the Pro-sp3TASSER server in CASP8
    • Zhou H, Pandit SB, Skolnick J. Performance of the Pro-sp3TASSER server in CASP8. Proteins 2009; 77: 123-127.
    • (2009) Proteins , vol.77 , pp. 123-127
    • Zhou, H.1    Pandit, S.B.2    Skolnick, J.3
  • 30
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method, for genomic fold recognition
    • McGuffin LJ, Jones DT. Improvement of the GenTHREADER method, for genomic fold recognition. Bioinformatics 2003; 19: 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.J.1    Jones, D.T.2
  • 31
    • 4143110064 scopus 로고    scopus 로고
    • Application of sparse NMR restraints to large-scale protein structure prediction
    • Li W, Zhang Y, Skolnik J. Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J 2004; 87: 1241-1248.
    • (2004) Biophys J , vol.87 , pp. 1241-1248
    • Li, W.1    Zhang, Y.2    Skolnik, J.3
  • 32
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997; 265: 217-241.
    • (1997) J Mol Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 33
    • 74249106219 scopus 로고    scopus 로고
    • I-TASSER: Fully automated protein structure prediction in CASP8
    • Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009; 77: 100-113.
    • (2009) Proteins , vol.77 , pp. 100-113
    • Zhang, Y.1
  • 34
    • 0033550256 scopus 로고    scopus 로고
    • Effective use of sequence correlation and conservation in fold recognition
    • Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999; 293: 1221-1239.
    • (1999) J Mol Biol , vol.293 , pp. 1221-1239
    • Olmea, O.1    Rost, B.2    Valencia, A.3
  • 35
    • 33847356936 scopus 로고    scopus 로고
    • A pairto-pair amino acids substitution matrix and its applications for protein structure prediction
    • Eyal E, Frenkel-Morgenstern M, Sobolev V, Pietrokovski S. A pairto-pair amino acids substitution matrix and its applications for protein structure prediction. Proteins 2007; 67: 142-153.
    • (2007) Proteins , vol.67 , pp. 142-153
    • Eyal, E.1    Frenkel-Morgenstern, M.2    Sobolev, V.3    Pietrokovski, S.4
  • 36
    • 47049101751 scopus 로고    scopus 로고
    • Using inferred residue contacts to distinguish, between correct and incorrect protein models
    • Miller CS, 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.S.1    Eisenberg, D.2
  • 37
    • 84860195568 scopus 로고    scopus 로고
    • CASP8 web pages; Available at: http://predictioncenter.org/download-area/ CASP8/predictions/RR.tar.gz.
  • 38
    • 74249104236 scopus 로고    scopus 로고
    • Domain definition and target classification, CASP8
    • Tress ML, Ezkurdia I, Richardson JS. Domain definition and target classification, CASP8. Proteins 2009; 77: 10-17.
    • (2009) Proteins , vol.77 , pp. 10-17
    • Tress, M.L.1    Ezkurdia, I.2    Richardson, J.S.3
  • 39
    • 0032605828 scopus 로고    scopus 로고
    • Processing and analysis of CASP3 protein structure predictions
    • Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999; 37: 22-29.
    • (1999) Proteins , vol.37 , pp. 22-29
    • Zemla, A.1    Venclovas, C.2    Moult, J.3    Fidelis, K.4
  • 40
    • 0042622381 scopus 로고    scopus 로고
    • 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
  • 41
    • 84860200431 scopus 로고    scopus 로고
    • CASP8 web pages; Available at: http://predictioncenter.org/casp8/index. cgi.
  • 42
    • 74249120024 scopus 로고    scopus 로고
    • Prediction of global and local quality of CASP8 models by MULTICOM series
    • Cheng J, Wang Z, Tegge AN, Eickholt J. Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 2009; 77: 181-184.
    • (2009) Proteins , vol.77 , pp. 181-184
    • Cheng, J.1    Wang, Z.2    Tegge, A.N.3    Eickholt, J.4
  • 43
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu S, Zhang Y. MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 2008; 72: 547-556.
    • (2008) Proteins , vol.72 , pp. 547-556
    • Wu, S.1    Zhang, Y.2
  • 45
    • 74249106002 scopus 로고    scopus 로고
    • The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins
    • Venclovas C, Margelevièius M. The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins. Proteins 2009; 77: 81-88.
    • (2009) Proteins , vol.77 , pp. 81-88
    • Venclovas, C.1    Margelevièius, M.2
  • 46
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009; 4: 363-371.
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 47
    • 74249103622 scopus 로고    scopus 로고
    • Assessment of global and local model quality in CASP8 using Pcons and ProQ
    • Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins 2009; 77: 167-172.
    • (2009) Proteins , vol.77 , pp. 167-172
    • Larsson, P.1    Skwark, M.J.2    Wallner, B.3    Elofsson, A.4
  • 48
    • 74249102516 scopus 로고    scopus 로고
    • Evaluation of CASP8 model quality predictions
    • Cozzetto D, Kryshtafovych A, Tramontano A. Evaluation of CASP8 model quality predictions. Proteins 2009; 77: 157-166.
    • (2009) Proteins , vol.77 , pp. 157-166
    • Cozzetto, D.1    Kryshtafovych, A.2    Tramontano, A.3
  • 49
    • 74249087111 scopus 로고    scopus 로고
    • Prediction of global and local model quality in CASP8 using the ModFOLD server
    • McGuffin LJ. Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins 2009; 77: 185-190.
    • (2009) Proteins , vol.77 , pp. 185-190
    • McGuffin, L.J.1
  • 50
    • 74249088516 scopus 로고    scopus 로고
    • Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
    • Benkert P, Tosatto SCE, Schwede T. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins 2009; 77: 173-180.
    • (2009) Proteins , vol.77 , pp. 173-180
    • Benkert, P.1    Tosatto, S.C.E.2    Schwede, T.3
  • 51
    • 74249085480 scopus 로고    scopus 로고
    • Applying undertaker to quality assessment
    • Archie JG, Paluszewski M, Karplus K. Applying undertaker to quality assessment. Proteins 2009; 77: 191-195.
    • (2009) Proteins , vol.77 , pp. 191-195
    • Archie, J.G.1    Paluszewski, M.2    Karplus, K.3
  • 52
    • 66149084059 scopus 로고    scopus 로고
    • Model quality assessment using distance constraints from alignments
    • Paluszewski M, Karplus K. Model quality assessment using distance constraints from alignments. Proteins 2009; 75: 540-549.
    • (2009) Proteins , vol.75 , pp. 540-549
    • Paluszewski, M.1    Karplus, K.2
  • 53
    • 66149136906 scopus 로고    scopus 로고
    • Applying undertaker cost functions to model quality assessment
    • Archie J, Karplus K. Applying undertaker cost functions to model quality assessment. Proteins 2009; 75: 550-555.
    • (2009) Proteins , vol.75 , pp. 550-555
    • Archie, J.1    Karplus, K.2
  • 54
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997; 265: 217-241,
    • (1997) J Mol Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.