메뉴 건너뛰기




Volumn 16, Issue 2, 2006, Pages 172-177

Comparative modeling for protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 33646002994     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2006.02.003     Document Type: Review
Times cited : (248)

References (46)
  • 1
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • A review of recent progress in de novo protein structure prediction.
    • Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871. A review of recent progress in de novo protein structure prediction.
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 2
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D., and Sali A. Protein structure prediction and structural genomics. Science 294 (2001) 93-96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 3
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., and Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J 5 (1986) 823-826
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 6
    • 17144425763 scopus 로고    scopus 로고
    • Practical lessons from protein structure prediction
    • This comprehensive review outlines currently available practical approaches to protein structure prediction, including recent advances in model quality assessment.
    • Ginalski K., Grishin N.V., Godzik A., and Rychlewski L. Practical lessons from protein structure prediction. Nucleic Acids Res 33 (2005) 1874-1891. This comprehensive review outlines currently available practical approaches to protein structure prediction, including recent advances in model quality assessment.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1874-1891
    • Ginalski, K.1    Grishin, N.V.2    Godzik, A.3    Rychlewski, L.4
  • 7
    • 4444298729 scopus 로고    scopus 로고
    • Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods
    • An evaluation of different profile-profile alignment methods.
    • Ohlson T., Wallner B., and Elofsson A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 57 (2004) 188-197. An evaluation of different profile-profile alignment methods.
    • (2004) Proteins , vol.57 , pp. 188-197
    • Ohlson, T.1    Wallner, B.2    Elofsson, A.3
  • 8
    • 2442663920 scopus 로고    scopus 로고
    • Scoring profile-to-profile sequence alignments
    • Wang G., and Dunbrack Jr. R.L. Scoring profile-to-profile sequence alignments. Protein Sci 13 (2004) 1612-1626
    • (2004) Protein Sci , vol.13 , pp. 1612-1626
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 9
    • 2342423130 scopus 로고    scopus 로고
    • Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
    • Sadreyev R.I., and Grishin N.V. Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics 20 (2004) 818-828
    • (2004) Bioinformatics , vol.20 , pp. 818-828
    • Sadreyev, R.I.1    Grishin, N.V.2
  • 10
    • 0347417008 scopus 로고    scopus 로고
    • Gaps in structurally similar proteins: towards improvement of multiple sequence alignment
    • Wrabl J.O., and Grishin N.V. Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. Proteins 54 (2004) 71-87
    • (2004) Proteins , vol.54 , pp. 71-87
    • Wrabl, J.O.1    Grishin, N.V.2
  • 11
    • 3442901082 scopus 로고    scopus 로고
    • Improving fold recognition without folds
    • Przybylski D., and Rost B. Improving fold recognition without folds. J Mol Biol 341 (2004) 255-269
    • (2004) J Mol Biol , vol.341 , pp. 255-269
    • Przybylski, D.1    Rost, B.2
  • 13
    • 30344459116 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP) - round VI
    • Moult J., Fidelis K., Tramontano A., Rost B., and Hubbard T. Critical assessment of methods of protein structure prediction (CASP) - round VI. Proteins (2005)
    • (2005) Proteins
    • Moult, J.1    Fidelis, K.2    Tramontano, A.3    Rost, B.4    Hubbard, T.5
  • 14
    • 30344475200 scopus 로고    scopus 로고
    • Progress over the first decade of CASP experiments
    • A description of the progress made in protein structure prediction during the course of the CASP experiments.
    • Kryshtafovych A., Venclovas C., Fidelis K., and Moult J. Progress over the first decade of CASP experiments. Proteins 61 suppl 7 (2005) 225-236. A description of the progress made in protein structure prediction during the course of the CASP experiments.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 225-236
    • Kryshtafovych, A.1    Venclovas, C.2    Fidelis, K.3    Moult, J.4
  • 15
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
    • This paper reviews the state of the art in protein structure prediction in the context of a decade of CASP experiments.
    • Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15 (2005) 285-289. This paper reviews the state of the art in protein structure prediction in the context of a decade of CASP experiments.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 285-289
    • Moult, J.1
  • 16
    • 30344447955 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP6 comparative modelling category
    • An assessment of the state of the art in comparative modeling from CASP6.
    • Tress M., Ezkurdia I., Grana O., Lopez G., and Valencia A. Assessment of predictions submitted for the CASP6 comparative modelling category. Proteins 61 suppl 7 (2005) 27-45. An assessment of the state of the art in comparative modeling from CASP6.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 27-45
    • Tress, M.1    Ezkurdia, I.2    Grana, O.3    Lopez, G.4    Valencia, A.5
  • 17
    • 0242267511 scopus 로고    scopus 로고
    • Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
    • Ginalski K., and Rychlewski L. Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins 53 suppl 6 (2003) 410-417
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 410-417
    • Ginalski, K.1    Rychlewski, L.2
  • 18
    • 30344454371 scopus 로고    scopus 로고
    • Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment and structure assessment
    • A report from one of the best performing groups in the comparative modeling category of CASP6.
    • Venclovas C., and Margelevicius M. Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment and structure assessment. Proteins 61 suppl 7 (2005) 99-105. A report from one of the best performing groups in the comparative modeling category of CASP6.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 99-105
    • Venclovas, C.1    Margelevicius, M.2
  • 19
    • 30344467519 scopus 로고    scopus 로고
    • Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models
    • Kolinski A., and Bujnicki J.M. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 61 suppl 7 (2005) 84-90
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 84-90
    • Kolinski, A.1    Bujnicki, J.M.2
  • 20
    • 25444458541 scopus 로고    scopus 로고
    • PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
    • Margelevicius M., and Venclovas C. PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. BMC Bioinformatics 6 (2005) 185
    • (2005) BMC Bioinformatics , vol.6 , pp. 185
    • Margelevicius, M.1    Venclovas, C.2
  • 21
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 356 (1992) 83-85
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 22
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 17 (1993) 355-362
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 23
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with Rosetta
    • A de novo method for modeling structurally variable regions in comparative models based on the Rosetta structure prediction algorithm is described and evaluated.
    • Rohl C.A., Strauss C.E., Chivian D., and Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55 (2004) 656-677. A de novo method for modeling structurally variable regions in comparative models based on the Rosetta structure prediction algorithm is described and evaluated.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 24
    • 0242299155 scopus 로고    scopus 로고
    • CAFASP3: the third critical assessment of fully automated structure prediction methods
    • Fischer D., Rychlewski L., Dunbrack Jr. R.L., Ortiz A.R., and Elofsson A. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 53 suppl 6 (2003) 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
  • 25
    • 11144241105 scopus 로고    scopus 로고
    • LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction
    • A report on the performance of protein structure prediction servers in the LiveBench-8 experiment.
    • Rychlewski L., and Fischer D. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci 14 (2005) 240-245. A report on the performance of protein structure prediction servers in the LiveBench-8 experiment.
    • (2005) Protein Sci , vol.14 , pp. 240-245
    • Rychlewski, L.1    Fischer, D.2
  • 28
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: a simple approach to improve protein structure predictions
    • Ginalski K., Elofsson A., Fischer D., and Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19 (2003) 1015-1018
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 29
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 51 (2003) 434-441
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 31
    • 30344456694 scopus 로고    scopus 로고
    • SPARKS 2 and SP(3) servers in CASP 6
    • Zhou H., and Zhou Y. SPARKS 2 and SP(3) servers in CASP 6. Proteins (2005)
    • (2005) Proteins
    • Zhou, H.1    Zhou, Y.2
  • 32
    • 10844286440 scopus 로고    scopus 로고
    • Relationship between multiple sequence alignments and quality of protein comparative models
    • The distribution of sequence identity in multiple sequence alignments is demonstrated to be a good estimator of the quality of comparative models.
    • Cozzetto D., and Tramontano A. Relationship between multiple sequence alignments and quality of protein comparative models. Proteins 58 (2005) 151-157. The distribution of sequence identity in multiple sequence alignments is demonstrated to be a good estimator of the quality of comparative models.
    • (2005) Proteins , vol.58 , pp. 151-157
    • Cozzetto, D.1    Tramontano, A.2
  • 33
    • 2542543509 scopus 로고    scopus 로고
    • Molecular modeling of protein function regions
    • The authors explore the usefulness of comparative models in deducing details of molecular function. They demonstrate that, in general, good insight into ligand binding can be obtained, providing there are no alignment errors.
    • DeWeese-Scott C., and Moult J. Molecular modeling of protein function regions. Proteins 55 (2004) 942-961. The authors explore the usefulness of comparative models in deducing details of molecular function. They demonstrate that, in general, good insight into ligand binding can be obtained, providing there are no alignment errors.
    • (2004) Proteins , vol.55 , pp. 942-961
    • DeWeese-Scott, C.1    Moult, J.2
  • 34
    • 4143110083 scopus 로고    scopus 로고
    • Systematic analysis of added-value in simple comparative models of protein structure
    • This study justifies the use of comparative models instead of templates to estimate structure-derived properties of proteins, showing that, in general, their added value increases with lower target-template sequence identity.
    • Chakravarty S., and Sanchez R. Systematic analysis of added-value in simple comparative models of protein structure. Structure 12 (2004) 1461-1470. This study justifies the use of comparative models instead of templates to estimate structure-derived properties of proteins, showing that, in general, their added value increases with lower target-template sequence identity.
    • (2004) Structure , vol.12 , pp. 1461-1470
    • Chakravarty, S.1    Sanchez, R.2
  • 35
    • 13744252339 scopus 로고    scopus 로고
    • Accuracy of structure-derived properties in simple comparative models of protein structures
    • ••], the authors show that the average accuracy of structure-derived properties of comparative models increases with higher target-template sequence identity. They also reveal that, for most properties, the differences observed between NMR and X-ray structures are similar to the errors in models based on templates with ∼40% sequence identity.
    • ••], the authors show that the average accuracy of structure-derived properties of comparative models increases with higher target-template sequence identity. They also reveal that, for most properties, the differences observed between NMR and X-ray structures are similar to the errors in models based on templates with ∼40% sequence identity.
    • (2005) Nucleic Acids Res , vol.33 , pp. 244-259
    • Chakravarty, S.1    Wang, L.2    Sanchez, R.3
  • 36
    • 27544504227 scopus 로고    scopus 로고
    • Evaluating the usefulness of protein structure models for molecular replacement
    • This study reveals that there is a clear relationship between the quality of comparative models and their suitability for molecular replacement. It also shows that target-template sequence identity is not a good diagnostic for the success of the procedure.
    • Giorgetti A., Raimondo D., Miele A.E., and Tramontano A. Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics 21 (2005) ii72-ii76. This study reveals that there is a clear relationship between the quality of comparative models and their suitability for molecular replacement. It also shows that target-template sequence identity is not a good diagnostic for the success of the procedure.
    • (2005) Bioinformatics , vol.21
    • Giorgetti, A.1    Raimondo, D.2    Miele, A.E.3    Tramontano, A.4
  • 37
    • 13844300063 scopus 로고    scopus 로고
    • Empirical limits for template-based protein structure prediction: the CASP5 example
    • An analysis of the empirical limits of template-based modeling of protein structure suggests that the methodology is approaching its limits for easy comparative modeling and that additional improvements in quality require information not available from template structures.
    • Contreras-Moreira B., Ezkurdia I., Tress M.L., and Valencia A. Empirical limits for template-based protein structure prediction: the CASP5 example. FEBS Lett 579 (2005) 1203-1207. An analysis of the empirical limits of template-based modeling of protein structure suggests that the methodology is approaching its limits for easy comparative modeling and that additional improvements in quality require information not available from template structures.
    • (2005) FEBS Lett , vol.579 , pp. 1203-1207
    • Contreras-Moreira, B.1    Ezkurdia, I.2    Tress, M.L.3    Valencia, A.4
  • 38
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y., and Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 101 (2004) 7594-7599
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 39
    • 14644438345 scopus 로고    scopus 로고
    • Progress and challenges in high-resolution refinement of protein structure models
    • Misura K.M., and Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 59 (2005) 15-29
    • (2005) Proteins , vol.59 , pp. 15-29
    • Misura, K.M.1    Baker, D.2
  • 40
    • 7444236378 scopus 로고    scopus 로고
    • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation
    • The authors present a novel approach to refining comparative models by free energy optimization along evolutionarily favored sampling directions. They show that improvement in model quality can be obtained.
    • Qian B., Ortiz A.R., and Baker D. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci USA 101 (2004) 15346-15351. The authors present a novel approach to refining comparative models by free energy optimization along evolutionarily favored sampling directions. They show that improvement in model quality can be obtained.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15346-15351
    • Qian, B.1    Ortiz, A.R.2    Baker, D.3
  • 41
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin N.V. Fold change in evolution of protein structures. J Struct Biol 134 (2001) 167-185
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 42
    • 0036600834 scopus 로고    scopus 로고
    • Evolution of protein structures and functions
    • Kinch L.N., and Grishin N.V. Evolution of protein structures and functions. Curr Opin Struct Biol 12 (2002) 400-408
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 400-408
    • Kinch, L.N.1    Grishin, N.V.2
  • 43
    • 2942585636 scopus 로고    scopus 로고
    • Progress towards mapping the universe of protein folds
    • Grant A., Lee D., and Orengo C. Progress towards mapping the universe of protein folds. Genome Biol 5 (2004) 107
    • (2004) Genome Biol , vol.5 , pp. 107
    • Grant, A.1    Lee, D.2    Orengo, C.3
  • 44
    • 26244437278 scopus 로고    scopus 로고
    • Protein family clustering for structural genomics
    • Yan Y., and Moult J. Protein family clustering for structural genomics. J Mol Biol 353 (2005) 744-759
    • (2005) J Mol Biol , vol.353 , pp. 744-759
    • Yan, Y.1    Moult, J.2
  • 45
    • 3042726394 scopus 로고    scopus 로고
    • Automatic target selection for structural genomics on eukaryotes
    • Liu J., Hegyi H., Acton T.B., Montelione G.T., and Rost B. Automatic target selection for structural genomics on eukaryotes. Proteins 56 (2004) 188-200
    • (2004) Proteins , vol.56 , pp. 188-200
    • Liu, J.1    Hegyi, H.2    Acton, T.B.3    Montelione, G.T.4    Rost, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.