메뉴 건너뛰기




Volumn 21, Issue 9, 2013, Pages 1531-1540

Protein modeling: What happened to the "protein structure gap"?

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYTOCHROME P450 2D6; MEMBRANE PROTEIN;

EID: 84883479032     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.08.007     Document Type: Review
Times cited : (107)

References (139)
  • 4
    • 48749103296 scopus 로고    scopus 로고
    • Integrating diverse data for structure determination of macromolecular assemblies
    • F. Alber, F. Förster, D. Korkin, M. Topf, and A. Sali Integrating diverse data for structure determination of macromolecular assemblies Annu. Rev. Biochem. 77 2008 443 477
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 443-477
    • Alber, F.1    Förster, F.2    Korkin, D.3    Topf, M.4    Sali, A.5
  • 6
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: Modelling protein interactions
    • P. Aloy, and R.B. Russell Structural systems biology: modelling protein interactions Nat. Rev. Mol. Cell Biol. 7 2006 188 197
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 8
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • K. Arnold, L. Bordoli, J. Kopp, and T. Schwede The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling Bioinformatics 22 2006 195 201
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 11
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 12
    • 79551613290 scopus 로고    scopus 로고
    • Toward the estimation of the absolute quality of individual protein structure models
    • P. Benkert, M. Biasini, and T. Schwede Toward the estimation of the absolute quality of individual protein structure models Bioinformatics 27 2011 343 350
    • (2011) Bioinformatics , vol.27 , pp. 343-350
    • Benkert, P.1    Biasini, M.2    Schwede, T.3
  • 14
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • DATABASE ISSUE
    • H. Berman, K. Henrick, H. Nakamura, and J.L. Markley The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 Database issue 2007 D301 D303
    • (2007) Nucleic Acids Res. , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 15
    • 84858126537 scopus 로고    scopus 로고
    • Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal
    • L. Bordoli, and T. Schwede Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal Methods Mol. Biol. 857 2012 107 136
    • (2012) Methods Mol. Biol. , vol.857 , pp. 107-136
    • Bordoli, L.1    Schwede, T.2
  • 17
    • 84878527131 scopus 로고    scopus 로고
    • Structural biology in situ - The potential of subtomogram averaging
    • J.A. Briggs Structural biology in situ - the potential of subtomogram averaging Curr. Opin. Struct. Biol. 23 2013 261 267
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 261-267
    • Briggs, J.A.1
  • 19
    • 76749112068 scopus 로고    scopus 로고
    • Disentangling direct from indirect co-evolution of residues in protein alignments
    • L. Burger, and E. van Nimwegen Disentangling direct from indirect co-evolution of residues in protein alignments PLoS Comput. Biol. 6 2010 e1000633
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 1000633
    • Burger, L.1    Van Nimwegen, E.2
  • 21
    • 84875200698 scopus 로고    scopus 로고
    • Functional implications of genome topology
    • G. Cavalli, and T. Misteli Functional implications of genome topology Nat. Struct. Mol. Biol. 20 2013 290 299
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 290-299
    • Cavalli, G.1    Misteli, T.2
  • 23
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • C. Chothia, and A.M. Lesk 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
  • 25
    • 0037464588 scopus 로고    scopus 로고
    • A vision for the future of genomics research
    • US National Human Genome Research Institute
    • F.S. Collins, E.D. Green, A.E. Guttmacher, M.S. Guyer US National Human Genome Research Institute A vision for the future of genomics research Nature 422 2003 835 847
    • (2003) Nature , vol.422 , pp. 835-847
    • Collins, F.S.1    Green, E.D.2    Guttmacher, A.E.3    Guyer, M.S.4
  • 26
    • 84878543095 scopus 로고    scopus 로고
    • Modeling G protein-coupled receptors and their interactions with ligands
    • S. Costanzi Modeling G protein-coupled receptors and their interactions with ligands Curr. Opin. Struct. Biol. 23 2013 185 190
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 185-190
    • Costanzi, S.1
  • 28
    • 84883209345 scopus 로고    scopus 로고
    • CSAR Benchmark Exercise 2011-2012: Evaluation of results from docking and relative ranking of blinded congeneric series
    • 10.1021/ci400025f Published online April 2, 2013
    • K.L. Damm-Ganamet, R.D. Smith, J.B. Dunbar Jr.; J.A. Stuckey, and H.A. Carlson CSAR Benchmark Exercise 2011-2012: Evaluation of results from docking and relative ranking of blinded congeneric series J. Chem. Inf. Model. 2013 10.1021/ci400025f Published online April 2, 2013
    • (2013) J. Chem. Inf. Model.
    • Damm-Ganamet, K.L.1    Smith, R.D.2    Dunbar, Jr.J.B.3    Stuckey, J.A.4    Carlson, H.A.5
  • 29
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • R. Das, and D. Baker Macromolecular modeling with rosetta Annu. Rev. Biochem. 77 2008 363 382
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 30
    • 84857790275 scopus 로고    scopus 로고
    • Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs
    • A. David, R. Razali, M.N. Wass, and M.J. Sternberg Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs Hum. Mutat. 33 2012 359 363
    • (2012) Hum. Mutat. , vol.33 , pp. 359-363
    • David, A.1    Razali, R.2    Wass, M.N.3    Sternberg, M.J.4
  • 31
    • 84875225476 scopus 로고    scopus 로고
    • Emerging methods in protein co-evolution
    • D. de Juan, F. Pazos, and A. Valencia Emerging methods in protein co-evolution Nat. Rev. Genet. 14 2013 249 261
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 249-261
    • De Juan, D.1    Pazos, F.2    Valencia, A.3
  • 32
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
    • J. Dekker, M.A. Marti-Renom, and L.A. Mirny Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data Nat. Rev. Genet. 14 2013 390 403
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 34
    • 84858374665 scopus 로고    scopus 로고
    • The amyloid state of proteins in human diseases
    • D. Eisenberg, and M. Jucker The amyloid state of proteins in human diseases Cell 148 2012 1188 1203
    • (2012) Cell , vol.148 , pp. 1188-1203
    • Eisenberg, D.1    Jucker, M.2
  • 37
    • 84876838711 scopus 로고    scopus 로고
    • The hierarchy of the 3D genome
    • J.H. Gibcus, and J. Dekker The hierarchy of the 3D genome Mol. Cell 49 2013 773 782
    • (2013) Mol. Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 38
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski 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
  • 39
    • 28544453561 scopus 로고    scopus 로고
    • Principles of selective ion transport in channels and pumps
    • E. Gouaux, and R. Mackinnon Principles of selective ion transport in channels and pumps Science 310 2005 1461 1465
    • (2005) Science , vol.310 , pp. 1461-1465
    • Gouaux, E.1    Mackinnon, R.2
  • 40
    • 84885861180 scopus 로고    scopus 로고
    • Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS)
    • 10.1016/j.sbi.2013.06.007 Published online July 5, 2013
    • M.A. Graewert, and D.I. Svergun Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS) Curr. Opin. Struct. Biol. 2013 10.1016/j.sbi.2013.06.007 Published online July 5, 2013
    • (2013) Curr. Opin. Struct. Biol.
    • Graewert, M.A.1    Svergun, D.I.2
  • 41
    • 69249212321 scopus 로고    scopus 로고
    • Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
    • N. Guex, M.C. Peitsch, and T. Schwede Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective Electrophoresis 30 Suppl 1 2009 S162 S173
    • (2009) Electrophoresis , vol.30 , Issue.SUPPL 1
    • Guex, N.1    Peitsch, M.C.2    Schwede, T.3
  • 42
    • 84883481556 scopus 로고    scopus 로고
    • The Protein Model Portal - A comprehensive resource for protein structure and model information
    • J. Haas, S. Roth, K. Arnold, F. Kiefer, T. Schmidt, L. Bordoli, and T. Schwede The Protein Model Portal - a comprehensive resource for protein structure and model information Database (Oxford) 2013 2013 bat031
    • (2013) Database (Oxford) , vol.2013 , pp. 031
    • Haas, J.1    Roth, S.2    Arnold, K.3    Kiefer, F.4    Schmidt, T.5    Bordoli, L.6    Schwede, T.7
  • 43
    • 84879934224 scopus 로고    scopus 로고
    • Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex
    • J. Hennig, I. Wang, M. Sonntag, F. Gabel, and M. Sattler Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex J. Biomol. NMR 56 2013 17 30
    • (2013) J. Biomol. NMR , vol.56 , pp. 17-30
    • Hennig, J.1    Wang, I.2    Sonntag, M.3    Gabel, F.4    Sattler, M.5
  • 44
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • A. Hildebrand, M. Remmert, A. Biegert, and J. Söding Fast and accurate automatic structure prediction with HHpred Proteins 77 Suppl 9 2009 128 132
    • (2009) Proteins , vol.77 , Issue.SUPPL 9 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Söding, J.4
  • 46
    • 84862647180 scopus 로고    scopus 로고
    • Three-dimensional structures of membrane proteins from genomic sequencing
    • T.A. Hopf, L.J. Colwell, R. Sheridan, B. Rost, C. Sander, and D.S. Marks Three-dimensional structures of membrane proteins from genomic sequencing Cell 149 2012 1607 1621
    • (2012) Cell , vol.149 , pp. 1607-1621
    • Hopf, T.A.1    Colwell, L.J.2    Sheridan, R.3    Rost, B.4    Sander, C.5    Marks, D.S.6
  • 47
    • 84872151549 scopus 로고    scopus 로고
    • Easy DNA modeling and more with GraphiteLifeExplorer
    • S. Hornus, B. Lévy, D. Larivière, and E. Fourmentin Easy DNA modeling and more with GraphiteLifeExplorer PLoS ONE 8 2013 e53609
    • (2013) PLoS ONE , vol.8 , pp. 53609
    • Hornus, S.1    Lévy, B.2    Larivière, D.3    Fourmentin, E.4
  • 48
    • 78149422216 scopus 로고    scopus 로고
    • Protein-protein docking tested in blind predictions: The CAPRI experiment
    • J. Janin Protein-protein docking tested in blind predictions: the CAPRI experiment Mol. Biosyst. 6 2010 2351 2362
    • (2010) Mol. Biosyst. , vol.6 , pp. 2351-2362
    • Janin, J.1
  • 49
    • 84873194008 scopus 로고    scopus 로고
    • Protein flexibility, not disorder, is intrinsic to molecular recognition
    • J. Janin, and M.J. Sternberg Protein flexibility, not disorder, is intrinsic to molecular recognition F1000 Biol. Rep. 5 2013 2
    • (2013) F1000 Biol. Rep. , vol.5 , pp. 2
    • Janin, J.1    Sternberg, M.J.2
  • 50
    • 84881115632 scopus 로고    scopus 로고
    • Tandem-repeat proteins: Regularity plus modularity equals design-ability
    • Y. Javadi, and L.S. Itzhaki Tandem-repeat proteins: regularity plus modularity equals design-ability Curr. Opin. Struct. Biol. 23 2013 622 631
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 622-631
    • Javadi, Y.1    Itzhaki, L.S.2
  • 51
    • 33244475355 scopus 로고    scopus 로고
    • Screening drug-like compounds by docking to homology models: A systematic study
    • V. Kairys, M.X. Fernandes, and M.K. Gilson Screening drug-like compounds by docking to homology models: a systematic study J. Chem. Inf. Model. 46 2006 365 379
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 365-379
    • Kairys, V.1    Fernandes, M.X.2    Gilson, M.K.3
  • 53
    • 84872225092 scopus 로고    scopus 로고
    • On the binding affinity of macromolecular interactions: Daring to ask why proteins interact
    • P.L. Kastritis, and A.M. Bonvin On the binding affinity of macromolecular interactions: daring to ask why proteins interact J. R. Soc. Interface 10 2013 20120835
    • (2013) J. R. Soc. Interface , vol.10 , pp. 20120835
    • Kastritis, P.L.1    Bonvin, A.M.2
  • 54
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • L.A. Kelley, and M.J. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nat. Protoc. 4 2009 363 371
    • (2009) Nat. Protoc. , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 58
    • 80855133462 scopus 로고    scopus 로고
    • CASP9 assessment of free modeling target predictions
    • L. Kinch, S. Yong Shi, Q. Cong, H. Cheng, Y. Liao, and N.V. Grishin CASP9 assessment of free modeling target predictions Proteins 79 Suppl 10 2011 59 73
    • (2011) Proteins , vol.79 , Issue.SUPPL 10 , pp. 59-73
    • Kinch, L.1    Yong Shi, S.2    Cong, Q.3    Cheng, H.4    Liao, Y.5    Grishin, N.V.6
  • 60
    • 38749131545 scopus 로고    scopus 로고
    • New G-protein-coupled receptor crystal structures: Insights and limitations
    • B. Kobilka, and G.F. Schertler New G-protein-coupled receptor crystal structures: insights and limitations Trends Pharmacol. Sci. 29 2008 79 83
    • (2008) Trends Pharmacol. Sci. , vol.29 , pp. 79-83
    • Kobilka, B.1    Schertler, G.F.2
  • 63
    • 84892964425 scopus 로고    scopus 로고
    • Assessment of the assessment: Evaluation of the model quality estimates in CASP10
    • 10.1002/prot.24347 Published June 18, 2013
    • A. Kryshtafovych, A. Barbato, K. Fidelis, B. Monastyrskyy, T. Schwede, and A. Tramontano Assessment of the assessment: Evaluation of the model quality estimates in CASP10 Proteins 2013 10.1002/prot.24347 Published June 18, 2013
    • (2013) Proteins
    • Kryshtafovych, A.1    Barbato, A.2    Fidelis, K.3    Monastyrskyy, B.4    Schwede, T.5    Tramontano, A.6
  • 64
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • GPCR Dock 2010 participants
    • I. Kufareva, M. Rueda, V. Katritch, R.C. Stevens, R. Abagyan GPCR Dock 2010 participants Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment Structure 19 2011 1108 1126
    • (2011) Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Stevens, R.C.4    Abagyan, R.5
  • 65
    • 84862233055 scopus 로고    scopus 로고
    • Templates are available to model nearly all complexes of structurally characterized proteins
    • P.J. Kundrotas, Z. Zhu, J. Janin, and I.A. Vakser Templates are available to model nearly all complexes of structurally characterized proteins Proc. Natl. Acad. Sci. USA 109 2012 9438 9441
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 9438-9441
    • Kundrotas, P.J.1    Zhu, Z.2    Janin, J.3    Vakser, I.A.4
  • 67
    • 79551598303 scopus 로고    scopus 로고
    • Improved predictions by Pcons net using multiple templates
    • P. Larsson, M.J. Skwark, B. Wallner, and A. Elofsson Improved predictions by Pcons.net using multiple templates Bioinformatics 27 2011 426 427
    • (2011) Bioinformatics , vol.27 , pp. 426-427
    • Larsson, P.1    Skwark, M.J.2    Wallner, B.3    Elofsson, A.4
  • 70
  • 71
    • 84862231127 scopus 로고    scopus 로고
    • Gene3D: A domain-based resource for comparative genomics, functional annotation and protein network analysis
    • DATABASE ISSUE
    • J. Lees, C. Yeats, J. Perkins, I. Sillitoe, R. Rentzsch, B.H. Dessailly, and C. Orengo Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis Nucleic Acids Res. 40 Database issue 2012 D465 D471
    • (2012) Nucleic Acids Res. , vol.40
    • Lees, J.1    Yeats, C.2    Perkins, J.3    Sillitoe, I.4    Rentzsch, R.5    Dessailly, B.H.6    Orengo, C.7
  • 72
    • 67650497792 scopus 로고    scopus 로고
    • Nature of the protein universe
    • M. Levitt Nature of the protein universe Proc. Natl. Acad. Sci. USA 106 2009 11079 11084
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 11079-11084
    • Levitt, M.1
  • 73
    • 79960189344 scopus 로고    scopus 로고
    • Dynamic allostery: Linkers are not merely flexible
    • B. Ma, C.J. Tsai, T. Haliloǧlu, and R. Nussinov Dynamic allostery: linkers are not merely flexible Structure 19 2011 907 917
    • (2011) Structure , vol.19 , pp. 907-917
    • Ma, B.1    Tsai, C.J.2    Haliloǧlu, T.3    Nussinov, R.4
  • 75
    • 80855132939 scopus 로고    scopus 로고
    • Assessment of template based protein structure predictions in CASP9
    • V. Mariani, F. Kiefer, T. Schmidt, J. Haas, and T. Schwede Assessment of template based protein structure predictions in CASP9 Proteins 79 Suppl 10 2011 37 58
    • (2011) Proteins , vol.79 , Issue.SUPPL 10 , pp. 37-58
    • Mariani, V.1    Kiefer, F.2    Schmidt, T.3    Haas, J.4    Schwede, T.5
  • 76
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • S.L. McGovern, and B.K. Shoichet Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J. Med. Chem. 46 2003 2895 2907
    • (2003) J. Med. Chem. , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 77
    • 84883470542 scopus 로고    scopus 로고
    • The ModFOLD4 server for the quality assessment of 3D protein models
    • L.J. McGuffin, M.T. Buenavista, and D.B. Roche The ModFOLD4 server for the quality assessment of 3D protein models Nucleic Acids Res. 41 W1 2013 W368 W372
    • (2013) Nucleic Acids Res. , vol.41 , Issue.W1
    • McGuffin, L.J.1    Buenavista, M.T.2    Roche, D.B.3
  • 79
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP) - Round IX
    • J. Moult, K. Fidelis, A. Kryshtafovych, and A. Tramontano Critical assessment of methods of protein structure prediction (CASP) - round IX Proteins 79 Suppl 10 2011 1 5
    • (2011) Proteins , vol.79 , Issue.SUPPL 10 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 81
    • 84862192588 scopus 로고    scopus 로고
    • Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis
    • T. Nugent, and D.T. Jones Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis Proc. Natl. Acad. Sci. USA 109 2012 E1540 E1547
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109
    • Nugent, T.1    Jones, D.T.2
  • 85
    • 0029004590 scopus 로고
    • Protein modeling by e-mail
    • M.C. Peitsch Protein modeling by e-mail Nat. Biotechnol. 13 1995 658 660
    • (1995) Nat. Biotechnol. , vol.13 , pp. 658-660
    • Peitsch, M.C.1
  • 88
    • 84877778935 scopus 로고    scopus 로고
    • Super-resolution in solution X-ray scattering and its applications to structural systems biology
    • R.P. Rambo, and J.A. Tainer Super-resolution in solution X-ray scattering and its applications to structural systems biology Annu. Rev. Biophys. 42 2013 415 441
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 415-441
    • Rambo, R.P.1    Tainer, J.A.2
  • 89
    • 84865844930 scopus 로고    scopus 로고
    • Improved model quality assessment using ProQ2
    • A. Ray, E. Lindahl, and B. Wallner Improved model quality assessment using ProQ2 BMC Bioinformatics 13 2012 224
    • (2012) BMC Bioinformatics , vol.13 , pp. 224
    • Ray, A.1    Lindahl, E.2    Wallner, B.3
  • 91
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • M. Remmert, A. Biegert, A. Hauser, and J. Söding HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment Nat. Methods 9 2012 173 175
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Söding, J.4
  • 92
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • W. Rieping, M. Habeck, and M. Nilges Inferential structure determination Science 309 2005 303 306
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 93
    • 78650352933 scopus 로고    scopus 로고
    • Quo vadis, virtual screening? A comprehensive survey of prospective applications
    • P. Ripphausen, B. Nisius, L. Peltason, and J. Bajorath Quo vadis, virtual screening? A comprehensive survey of prospective applications J. Med. Chem. 53 2010 8461 8467
    • (2010) J. Med. Chem. , vol.53 , pp. 8461-8467
    • Ripphausen, P.1    Nisius, B.2    Peltason, L.3    Bajorath, J.4
  • 94
    • 37249065351 scopus 로고    scopus 로고
    • The molecular sociology of the cell
    • C.V. Robinson, A. Sali, and W. Baumeister The molecular sociology of the cell Nature 450 2007 973 982
    • (2007) Nature , vol.450 , pp. 973-982
    • Robinson, C.V.1    Sali, A.2    Baumeister, W.3
  • 95
    • 79959564695 scopus 로고    scopus 로고
    • The IntFOLD server: An integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
    • WEB SERVER ISSUE
    • D.B. Roche, M.T. Buenavista, S.J. Tetchner, and L.J. McGuffin The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction Nucleic Acids Res. 39 Web Server issue 2011 W171 W176
    • (2011) Nucleic Acids Res. , vol.39
    • Roche, D.B.1    Buenavista, M.T.2    Tetchner, S.J.3    McGuffin, L.J.4
  • 97
    • 84856497340 scopus 로고    scopus 로고
    • Putting the pieces together: Integrative modeling platform software for structure determination of macromolecular assemblies
    • D. Russel, K. Lasker, B. Webb, J. Velázquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, and A. Sali Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies PLoS Biol. 10 2012 e1001244
    • (2012) PLoS Biol. , vol.10 , pp. 1001244
    • Russel, D.1    Lasker, K.2    Webb, B.3    Velázquez-Muriel, J.4    Tjioe, E.5    Schneidman-Duhovny, D.6    Peterson, B.7    Sali, A.8
  • 98
    • 11144241105 scopus 로고    scopus 로고
    • LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
    • L. Rychlewski, and D. Fischer LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction Protein Sci. 14 2005 240 245
    • (2005) Protein Sci. , vol.14 , pp. 240-245
    • Rychlewski, L.1    Fischer, D.2
  • 99
    • 84862876863 scopus 로고    scopus 로고
    • Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA
    • M. Safi, and R.H. Lilien Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA J. Chem. Inf. Model. 52 2012 1529 1541
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1529-1541
    • Safi, M.1    Lilien, R.H.2
  • 100
    • 77956406949 scopus 로고    scopus 로고
    • Proceedings of the Third Annual Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) Challenge and Workshop. June 2009. Montreal, Canada
    • SAMPL
    • SAMPL Proceedings of the Third Annual Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) Challenge and Workshop. June 2009. Montreal, Canada J. Comput. Aided Mol. Des. 24 2010 257 383
    • (2010) J. Comput. Aided Mol. Des. , vol.24 , pp. 257-383
  • 101
    • 0032506030 scopus 로고    scopus 로고
    • Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
    • R. Sánchez, and A. Sali Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc. Natl. Acad. Sci. USA 95 1998 13597 13602
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 13597-13602
    • Sánchez, R.1    Sali, A.2
  • 102
    • 79851511415 scopus 로고    scopus 로고
    • Macromolecular docking restrained by a small angle X-ray scattering profile
    • D. Schneidman-Duhovny, M. Hammel, and A. Sali Macromolecular docking restrained by a small angle X-ray scattering profile J. Struct. Biol. 173 2011 461 471
    • (2011) J. Struct. Biol. , vol.173 , pp. 461-471
    • Schneidman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 103
    • 84865525834 scopus 로고    scopus 로고
    • Integrative structural modeling with small angle X-ray scattering profiles
    • D. Schneidman-Duhovny, S.J. Kim, and A. Sali Integrative structural modeling with small angle X-ray scattering profiles BMC Struct. Biol. 12 2012 17
    • (2012) BMC Struct. Biol. , vol.12 , pp. 17
    • Schneidman-Duhovny, D.1    Kim, S.J.2    Sali, A.3
  • 106
    • 84864116955 scopus 로고    scopus 로고
    • RNA structure prediction: An overview of methods
    • M.G. Seetin, and D.H. Mathews RNA structure prediction: an overview of methods Methods Mol. Biol. 905 2012 99 122
    • (2012) Methods Mol. Biol. , vol.905 , pp. 99-122
    • Seetin, M.G.1    Mathews, D.H.2
  • 107
    • 58149468410 scopus 로고    scopus 로고
    • De novo protein structure generation from incomplete chemical shift assignments
    • Y. Shen, R. Vernon, D. Baker, and A. Bax De novo protein structure generation from incomplete chemical shift assignments J. Biomol. NMR 43 2009 63 78
    • (2009) J. Biomol. NMR , vol.43 , pp. 63-78
    • Shen, Y.1    Vernon, R.2    Baker, D.3    Bax, A.4
  • 110
    • 84878553777 scopus 로고    scopus 로고
    • Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
    • J. Skolnick, H. Zhou, and M. Gao Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr. Opin. Struct. Biol. 23 2013 191 197
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 191-197
    • Skolnick, J.1    Zhou, H.2    Gao, M.3
  • 111
    • 79953071469 scopus 로고    scopus 로고
    • Three-dimensional modeling of protein interactions and complexes is going 'omics
    • A. Stein, R. Mosca, and P. Aloy Three-dimensional modeling of protein interactions and complexes is going 'omics Curr. Opin. Struct. Biol. 21 2011 200 208
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 200-208
    • Stein, A.1    Mosca, R.2    Aloy, P.3
  • 112
    • 0001433241 scopus 로고
    • Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
    • M.J. Sutcliffe, I. Haneef, D. Carney, and T.L. Blundell Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures Protein Eng. 1 1987 377 384
    • (1987) Protein Eng. , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 116
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • DATABASE ISSUE UniProt Consortium
    • UniProt Consortium Update on activities at the Universal Protein Resource (UniProt) in 2013 Nucleic Acids Res. 41 Database issue 2013 D43 D47
    • (2013) Nucleic Acids Res. , vol.41
  • 118
    • 84873198878 scopus 로고    scopus 로고
    • The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure
    • V.N. Uversky, and A.K. Dunker The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure F1000 Biol. Rep. 5 2013 1
    • (2013) F1000 Biol. Rep. , vol.5 , pp. 1
    • Uversky, V.N.1    Dunker, A.K.2
  • 119
    • 84878552481 scopus 로고    scopus 로고
    • Low-resolution structural modeling of protein interactome
    • I.A. Vakser Low-resolution structural modeling of protein interactome Curr. Opin. Struct. Biol. 23 2013 198 205
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 198-205
    • Vakser, I.A.1
  • 121
    • 79251640891 scopus 로고    scopus 로고
    • An inventory of the bacterial macromolecular components and their spatial organization
    • A. Vendeville, D. Larivière, and E. Fourmentin An inventory of the bacterial macromolecular components and their spatial organization FEMS Microbiol. Rev. 35 2011 395 414
    • (2011) FEMS Microbiol. Rev. , vol.35 , pp. 395-414
    • Vendeville, A.1    Larivière, D.2    Fourmentin, E.3
  • 122
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • M. Vidal, M.E. Cusick, and A.L. Barabási Interactome networks and human disease Cell 144 2011 986 998
    • (2011) Cell , vol.144 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.L.3
  • 124
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • J.J. Ward, J.S. Sodhi, L.J. McGuffin, B.F. Buxton, and D.T. Jones Prediction and functional analysis of native disorder in proteins from the three kingdoms of life J. Mol. Biol. 337 2004 635 645
    • (2004) J. Mol. Biol. , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 125
    • 84874181173 scopus 로고    scopus 로고
    • Biochemistry. Integrative structural biology
    • A.B. Ward, A. Sali, and I.A. Wilson Biochemistry. Integrative structural biology Science 339 2013 913 915
    • (2013) Science , vol.339 , pp. 913-915
    • Ward, A.B.1    Sali, A.2    Wilson, I.A.3
  • 126
    • 79958064379 scopus 로고    scopus 로고
    • Challenges for the prediction of macromolecular interactions
    • M.N. Wass, A. David, and M.J. Sternberg Challenges for the prediction of macromolecular interactions Curr. Opin. Struct. Biol. 21 2011 382 390
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 382-390
    • Wass, M.N.1    David, A.2    Sternberg, M.J.3
  • 127
    • 0038497542 scopus 로고
    • Molecular structure of nucleic acids; A structure for deoxyribose nucleic acid
    • J.D. Watson, and F.H. Crick Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid Nature 171 1953 737 738
    • (1953) Nature , vol.171 , pp. 737-738
    • Watson, J.D.1    Crick, F.H.2
  • 129
    • 84872531476 scopus 로고    scopus 로고
    • Prediction of phenotypes of missense mutations in human proteins from biological assemblies
    • Q. Wei, Q. Xu, and R.L. Dunbrack Jr. Prediction of phenotypes of missense mutations in human proteins from biological assemblies Proteins 81 2013 199 213
    • (2013) Proteins , vol.81 , pp. 199-213
    • Wei, Q.1    Xu, Q.2    Dunbrack, Jr.R.L.3
  • 130
    • 84859455527 scopus 로고    scopus 로고
    • Structure-based model of allostery predicts coupling between distant sites
    • P. Weinkam, J. Pons, and A. Sali Structure-based model of allostery predicts coupling between distant sites Proc. Natl. Acad. Sci. USA 109 2012 4875 4880
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 4875-4880
    • Weinkam, P.1    Pons, J.2    Sali, A.3
  • 131
    • 84874032378 scopus 로고    scopus 로고
    • Computational design of novel protein binders and experimental affinity maturation
    • T.A. Whitehead, D. Baker, and S.J. Fleishman Computational design of novel protein binders and experimental affinity maturation Methods Enzymol. 523 2013 1 19
    • (2013) Methods Enzymol. , vol.523 , pp. 1-19
    • Whitehead, T.A.1    Baker, D.2    Fleishman, S.J.3
  • 132
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • WEB SERVER ISSUE
    • M. Wiederstein, and M.J. Sippl ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res. 35 Web Server issue 2007 W407 W410
    • (2007) Nucleic Acids Res. , vol.35
    • Wiederstein, M.1    Sippl, M.J.2
  • 133
    • 78651306870 scopus 로고    scopus 로고
    • The protein common interface database (ProtCID) - A comprehensive database of interactions of homologous proteins in multiple crystal forms
    • DATABASE ISSUE
    • Q. Xu, and R.L. Dunbrack Jr. The protein common interface database (ProtCID) - a comprehensive database of interactions of homologous proteins in multiple crystal forms Nucleic Acids Res. 39 Database issue 2011 D761 D770
    • (2011) Nucleic Acids Res. , vol.39
    • Xu, Q.1    Dunbrack, Jr.R.L.2
  • 134
    • 80053563027 scopus 로고    scopus 로고
    • Cryo-electron tomography: Gaining insight into cellular processes by structural approaches
    • T. Yahav, T. Maimon, E. Grossman, I. Dahan, and O. Medalia Cryo-electron tomography: gaining insight into cellular processes by structural approaches Curr. Opin. Struct. Biol. 21 2011 670 677
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 670-677
    • Yahav, T.1    Maimon, T.2    Grossman, E.3    Dahan, I.4    Medalia, O.5
  • 137
    • 84893010893 scopus 로고    scopus 로고
    • Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10
    • 10.1002/prot.24341 Published June 13, 2013
    • Y. Zhang Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10 Proteins 2013 10.1002/prot.24341 Published June 13, 2013
    • (2013) Proteins
    • Zhang, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.