-
1
-
-
24944493938
-
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
-
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
-
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
-
4
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom M.A., Stuart A.C., Fiser A., Sanchez R., Melo F., and Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29 (2000) 291-325
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
5
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 (1997) 3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
6
-
-
17144425763
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
26
-
-
0043123211
-
EVA: evaluation of protein structure prediction servers
-
Koh I.Y., Eyrich V.A., Marti-Renom M.A., Przybylski D., Madhusudhan M.S., Eswar N., Grana O., Pazos F., Valencia A., Sali A., et al. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 31 (2003) 3311-3315
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3311-3315
-
-
Koh, I.Y.1
Eyrich, V.A.2
Marti-Renom, M.A.3
Przybylski, D.4
Madhusudhan, M.S.5
Eswar, N.6
Grana, O.7
Pazos, F.8
Valencia, A.9
Sali, A.10
-
27
-
-
13444270892
-
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
-
Deshpande N., Addess K.J., Bluhm W.F., Merino-Ott J.C., Townsend-Merino W., Zhang Q., Knezevich C., Xie L., Chen L., Feng Z., et al. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 33 (2005) D233-D237
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Deshpande, N.1
Addess, K.J.2
Bluhm, W.F.3
Merino-Ott, J.C.4
Townsend-Merino, W.5
Zhang, Q.6
Knezevich, C.7
Xie, L.8
Chen, L.9
Feng, Z.10
-
28
-
-
0038386050
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
46
-
-
0033764251
-
Protein structure modeling for structural genomics
-
Sanchez R., Pieper U., Melo F., Eswar N., Marti-Renom M.A., Madhusudhan M.S., Mirkovic N., and Sali A. Protein structure modeling for structural genomics. Nat Struct Biol 7 suppl (2000) 986-990
-
(2000)
Nat Struct Biol
, vol.7
, Issue.SUPPL
, pp. 986-990
-
-
Sanchez, R.1
Pieper, U.2
Melo, F.3
Eswar, N.4
Marti-Renom, M.A.5
Madhusudhan, M.S.6
Mirkovic, N.7
Sali, A.8
|