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Volumn 53, Issue SUPPL. 6, 2003, Pages 436-456

Predictions Without Templates: New Folds, Secondary Structure, and Contacts in CASP5

Author keywords

CASP5 assessment; De novo ab initio structure prediction; Residue residue contacts; Secondary structure

Indexed keywords

CASP4 MODEL; CASP5 TARGET; CONFERENCE PAPER; DIAGNOSTIC ACCURACY; DNA TEMPLATE; MODEL; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TARGETING; STRUCTURE ANALYSIS;

EID: 0242299187     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10546     Document Type: Conference Paper
Times cited : (92)

References (34)
  • 1
    • 0028849882 scopus 로고
    • Evaluation of current techniques for ab initio protein structure prediction
    • Defay T, Cohen FE. Evaluation of current techniques for ab initio protein structure prediction. Proteins 1995;23:431-445.
    • (1995) Proteins , vol.23 , pp. 431-445
    • Defay, T.1    Cohen, F.E.2
  • 2
    • 0031307080 scopus 로고    scopus 로고
    • CASP2: Report on ab initio predictions
    • Lesk AM. CASP2: report on ab initio predictions. Proteins 1997; Suppl 1:151-166.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 151-166
    • Lesk, A.M.1
  • 3
    • 0032828469 scopus 로고    scopus 로고
    • Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    • Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999;Suppl 3:149-170.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 149-170
    • Orengo, C.A.1    Bray, J.E.2    Hubbard, T.3    LoConte, L.4    Sillitoe, I.5
  • 4
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: Predictions of three-dimensional structures, secondary structures, and interresidue contacts
    • Lesk AM, Lo Conte L, Hubbard TJ. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins 2001; Suppl 5:98-118.
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 98-118
    • Lesk, A.M.1    Lo Conte, L.2    Hubbard, T.J.3
  • 5
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281:565-577.
    • (1998) J Mol Biol , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 6
    • 0031298075 scopus 로고    scopus 로고
    • Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs
    • Jones DT. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins 1997;Suppl 1:185-191.
    • (1997) Proteins , Issue.SUPPL. 1 , pp. 185-191
    • Jones, D.T.1
  • 8
    • 0036385826 scopus 로고    scopus 로고
    • Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation
    • Fukushima K, Kikuchi J, Koshiba S, Kigawa T, Kuroda Y, Yokoyama S. Solution structure of the DFF-C domain of DFF45/ICAD. A structural basis for the regulation of apoptotic DNA fragmentation. J Mol Biol 2002;321:317-327.
    • (2002) J Mol Biol , vol.321 , pp. 317-327
    • Fukushima, K.1    Kikuchi, J.2    Koshiba, S.3    Kigawa, T.4    Kuroda, Y.5    Yokoyama, S.6
  • 9
    • 0018350099 scopus 로고
    • Gene duplications in the structural evolution of chymotrypsin
    • MacLachlan AD. Gene duplications in the structural evolution of chymotrypsin. J Mol Biol 1979;128:49-79.
    • (1979) J Mol Biol , vol.128 , pp. 49-79
    • MacLachlan, A.D.1
  • 10
    • 0032606104 scopus 로고    scopus 로고
    • RMS/coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
    • Hubbard TJ. RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. Proteins 1999;Suppl 3:15-21.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 15-21
    • Hubbard, T.J.1
  • 11
    • 0033081846 scopus 로고    scopus 로고
    • A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment
    • Zemla A, Venclovas C, Fidelis K, Rost B. A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins 1999;34:220-223.
    • (1999) Proteins , vol.34 , pp. 220-223
    • Zemla, A.1    Venclovas, C.2    Fidelis, K.3    Rost, B.4
  • 12
    • 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;Suppl 3:22-29.
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 22-29
    • Zemla, A.1    Venclovas, C.2    Moult, J.3    Fidelis, K.4
  • 14
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell RB, Barton GJ. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 1992;14:309-323.
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 16
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 18
    • 0028064006 scopus 로고
    • Redefining the goals of protein secondary structure prediction
    • Rost B, Sander C, Schneider R. Redefining the goals of protein secondary structure prediction. J Mol Biol 1994;235:13-26.
    • (1994) J Mol Biol , vol.235 , pp. 13-26
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 19
    • 0020997912 scopus 로고
    • 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
  • 20
    • 0242330730 scopus 로고    scopus 로고
    • Assessment of homology based predictions in CASP5
    • Tramontano A, Morea V, Assessment of homology based predictions in CASP5. Proteins 2003;Suppl 6:352-368.
    • (2003) Proteins , Issue.SUPPL. 6 , pp. 352-368
    • Tramontano, A.1    Morea, V.2
  • 21
    • 0033369033 scopus 로고    scopus 로고
    • Exploiting the past and the future in protein secondary structure prediction
    • Baldi P, Brunak S, Frasconi P, Soda G, Pollastri G. Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 1999;15:937-946.
    • (1999) Bioinformatics , vol.15 , pp. 937-946
    • Baldi, P.1    Brunak, S.2    Frasconi, P.3    Soda, G.4    Pollastri, G.5
  • 25
    • 0021097529 scopus 로고
    • How good are predictions of protein secondary structure?
    • Kabsch W, Sander C. How good are predictions of protein secondary structure? FEBS Lett 1983;155:179-182.
    • (1983) FEBS Lett , vol.155 , pp. 179-182
    • Kabsch, W.1    Sander, C.2
  • 26
    • 0027765576 scopus 로고
    • The limits of protein secondary structure prediction accuracy from multiple sequence alignment
    • Russell RB, Barton GJ. The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J Mol Biol 1993;234:951-957.
    • (1993) J Mol Biol , vol.234 , pp. 951-957
    • Russell, R.B.1    Barton, G.J.2
  • 27
    • 0035698737 scopus 로고    scopus 로고
    • EVA: Large-scale analysis of secondary structure prediction
    • Rost B, Eyrich VA. EVA: large-scale analysis of secondary structure prediction. Proteins 2001;Suppl 5:192-199.
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 192-199
    • Rost, B.1    Eyrich, V.A.2
  • 30
    • 0035237804 scopus 로고    scopus 로고
    • 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. Bioinformatics 2001;17 Suppl 1:S234-S242.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3    Casadio, R.4
  • 31
    • 0034604368 scopus 로고    scopus 로고
    • HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins
    • Bystroff C, Thorsson V, Baker D. HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. J Mol Biol 2000;301:173-190.
    • (2000) J Mol Biol , vol.301 , pp. 173-190
    • Bystroff, C.1    Thorsson, V.2    Baker, D.3
  • 32
    • 0042721397 scopus 로고    scopus 로고
    • Predicting inter-residue contacts using templates and pathways
    • Shao Y, Bystroff C. Predicting inter-residue contacts using templates and pathways. Proteins 2003;Suppl 6:497-502.
    • (2003) Proteins , Issue.SUPPL. 6 , pp. 497-502
    • Shao, Y.1    Bystroff, C.2
  • 33
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.
    • (1991) J Appl Crystallogr , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 34
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
    • (1997) Methods Enzymol , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.