메뉴 건너뛰기




Volumn , Issue , 2011, Pages 255-279

Genome-wide protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84874593309     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-6889-0_11     Document Type: Chapter
Times cited : (7)

References (107)
  • 1
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy P, Querol E, Aviles F, Sternberg J (2001) Automated structure based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311:395-408
    • (2001) J Mol Biol , vol.311 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.3    Sternberg, J.4
  • 3
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 4
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93-96
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 7
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016):164-170
    • (1991) Science , vol.253 , Issue.5016 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 8
    • 24944493938 scopus 로고    scopus 로고
    • Towards high-resolution de novo structure prediction for small proteins
    • Bradley P, Misuara K, Baker D (2005) Towards high-resolution de novo structure prediction for small proteins. Science 309:1868-1871
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misuara, K.2    Baker, D.3
  • 9
    • 0037391107 scopus 로고    scopus 로고
    • Membrane protein crystallization
    • Caffrey M (2003) Membrane protein crystallization. J Struct Biol 142:108-132
    • (2003) J Struct Biol , vol.142 , pp. 108-132
    • Caffrey, M.1
  • 10
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 12:2001-2014
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.3
  • 11
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: Expectations and outcomes
    • Chandonia J, Brenner S (2006) The impact of structural genomics: expectations and outcomes. Science 311:347-351
    • (2006) Science , vol.311 , pp. 347-351
    • Chandonia, J.1    Brenner, S.2
  • 12
    • 20144377620 scopus 로고    scopus 로고
    • Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    • Chen H, Zhou HX (2005a) Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res 33(10):3193-3199
    • (2005) Nucleic Acids Res , vol.33 , Issue.10 , pp. 3193-3199
    • Chen, H.1    Zhou, H.X.2
  • 13
    • 21744440928 scopus 로고    scopus 로고
    • Identification and pharmacological characterization of prokineticin 2beta as a selective ligand for prokineticin receptor 1
    • Chen J, Kuei C, Sutton S, Wilson S, Yu J, Kamme F, Mazur C, Lovenberg T, Liu C (2005b) Identification and pharmacological characterization of prokineticin 2beta as a selective ligand for prokineticin receptor 1. Mol Pharmacol 67:2070-2076
    • (2005) Mol Pharmacol , vol.67 , pp. 2070-2076
    • Chen, J.1    Kuei, C.2    Sutton, S.3    Wilson, S.4    Yu, J.5    Kamme, F.6    Mazur, C.7    Lovenberg, T.8    Liu, C.9
  • 14
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    • Cheng J, Baldi P (2005) Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21(Suppl 1):i75-84
    • (2005) Bioinformatics , vol.21 , pp. i75-i84
    • Cheng, J.1    Baldi, P.2
  • 15
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • Cheng J, Baldi P (2007) Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 8:113
    • (2007) BMC Bioinformatics , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 17
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews J (2000) Drug discovery: a historical perspective. Science 287(5460):1960-1964
    • (2000) Science , vol.287 , Issue.5460 , pp. 1960-1964
    • Drews, J.1
  • 19
    • 0030724017 scopus 로고    scopus 로고
    • Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
    • Fischer D, Eisenberg D (1997) Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci 94:11929-11934
    • (1997) Proc Natl Acad Sci , vol.94 , pp. 11929-11934
    • Fischer, D.1    Eisenberg, D.2
  • 20
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 21
    • 0032735188 scopus 로고    scopus 로고
    • Modelling G-protein-coupled receptors for drug design
    • Flower DR (1999) Modelling G-protein-coupled receptors for drug design. Biochim Biophys Acta 1422:207-234
    • (1999) Biochim Biophys Acta , vol.1422 , pp. 207-234
    • Flower, D.R.1
  • 23
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566-579
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 25
    • 34250376066 scopus 로고    scopus 로고
    • Structure and conformational changes in the C-terminal domain of the beta2-adrenoceptor: Insights from fluorescence resonance energy transfer studies
    • Granier S, Kim S, Shafer AM, Ratnala VR, Fung JJ, Zare RN, Kobilka B (2007) Structure and conformational changes in the C-terminal domain of the beta2-adrenoceptor: insights from fluorescence resonance energy transfer studies. J Biol Chem 282:13895-13905
    • (2007) J Biol Chem , vol.282 , pp. 13895-13905
    • Granier, S.1    Kim, S.2    Shafer, A.M.3    Ratnala, V.R.4    Fung, J.J.5    Zare, R.N.6    Kobilka, B.7
  • 27
    • 0029117219 scopus 로고
    • Identification of critical determinants of alpha 1-adrenergic receptor subtype selective agonist binding
    • Hwa J, Graham RM, Perez DM (1995) Identification of critical determinants of alpha 1-adrenergic receptor subtype selective agonist binding. J Biol Chem 270:23189-23195
    • (1995) J Biol Chem , vol.270 , pp. 23189-23195
    • Hwa, J.1    Graham, R.M.2    Perez, D.M.3
  • 29
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.1
  • 30
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358(6381):86-89
    • (1992) Nature , vol.358 , Issue.6381 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 31
    • 0028211273 scopus 로고
    • A model recognition approach to the prediction of all-helical membrane protein structure and topology
    • Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33(10):3038-3049
    • (1994) Biochemistry , vol.33 , Issue.10 , pp. 3038-3049
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 32
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14(10):846-856
    • (1998) Bioinformatics , vol.14 , Issue.10 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 33
    • 0035964191 scopus 로고    scopus 로고
    • TOUCHSTONE: An ab initio protein structure prediction method that uses threading based tertiary restraints
    • Kihara D, Lu H, Kolinski A, Skolnick J (2001) TOUCHSTONE: an ab initio protein structure prediction method that uses threading based tertiary restraints Proc Natl Acad Sci 98:10125-10130
    • (2001) Proc Natl Acad Sci , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 34
    • 0037197857 scopus 로고    scopus 로고
    • Ab initio protein structure prediction on a genomic scale: Application to Mycoplasma genitalim genome
    • Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J (2002) Ab initio protein structure prediction on a genomic scale: application to Mycoplasma genitalim genome. Proc Natl Acad Sci 99:5993-5998
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 5993-5998
    • Kihara, D.1    Zhang, Y.2    Lu, H.3    Kolinski, A.4    Skolnick, J.5
  • 35
    • 12944263648 scopus 로고    scopus 로고
    • Ab initio prediction of the three-dimensional structure of a de novo designed protein: A double-blind case study
    • Klepeis JL, Wei Y, Hecht MH, Floudas CA (2005) Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 58:560-570
    • (2005) Proteins , vol.58 , pp. 560-570
    • Klepeis, J.L.1    Wei, Y.2    Hecht, M.H.3    Floudas, C.A.4
  • 36
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt GJ (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285:1887-1897
    • (1999) J Mol Biol , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 37
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • Kolinski A, Skolnick J (1994) Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352
    • (1994) Proteins , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 38
    • 36749099341 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions for template-based modeling targets
    • Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins 69(Suppl 8):38-56
    • (2007) Proteins , vol.69 , pp. 38-56
    • Kopp, J.1    Bordoli, L.2    Battey, J.N.3    Kiefer, F.4    Schwede, T.5
  • 39
    • 0034704105 scopus 로고    scopus 로고
    • Coordinated up-regulation by hypoxia of adrenomedullin and one of its putative receptors (RDC-1) in cells of the rat blood-brain barrier
    • Ladoux A, Frelin C (2000) Coordinated up-regulation by hypoxia of adrenomedullin and one of its putative receptors (RDC-1) in cells of the rat blood-brain barrier. J Biol Chem 275:39914-39919
    • (2000) J Biol Chem , vol.275 , pp. 39914-39919
    • Ladoux, A.1    Frelin, C.2
  • 40
    • 68049138029 scopus 로고    scopus 로고
    • REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks
    • Li Y, Zhang Y (2009) REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 76(3):665-676
    • (2009) Proteins , vol.76 , Issue.3 , pp. 665-676
    • Li, Y.1    Zhang, Y.2
  • 41
    • 0033545962 scopus 로고    scopus 로고
    • Protein structure prediction by global optimization of a potential energy function
    • Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA (1999) Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 96(10):5482-5485
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.10 , pp. 5482-5485
    • Liwo, A.1    Lee, J.2    Ripoll, D.R.3    Pillardy, J.4    Scheraga, H.A.5
  • 42
    • 36748998785 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP7 function prediction category
    • Lopez G, Rojas A, Tress M, Valencia A (2007) Assessment of predictions submitted for the CASP7 function prediction category. Proteins 69(Suppl 8):165-174
    • (2007) Proteins , vol.69 , pp. 165-174
    • Lopez, G.1    Rojas, A.2    Tress, M.3    Valencia, A.4
  • 43
    • 22844448355 scopus 로고    scopus 로고
    • Structural biology of G protein-coupled receptors
    • Lundstrom K (2005) Structural biology of G protein-coupled receptors. Bioorg Med Chem Lett 15:3654-3657
    • (2005) Bioorg Med Chem Lett , vol.15 , pp. 3654-3657
    • Lundstrom, K.1
  • 44
    • 38149027753 scopus 로고    scopus 로고
    • Insight into disulfide bond catalysis in Chlamydia from the structure and function of DsbH, a novel oxidoreductase
    • MacTT, Von Hacht A, Hung KC, Dutton RJ, Boyd D, Bardwell JC, Ulmer TS (2008) Insight into disulfide bond catalysis in Chlamydia from the structure and function of DsbH, a novel oxidoreductase. J Biol Chem 283:824-832
    • (2008) J Biol Chem , vol.283 , pp. 824-832
    • Mac, T.T.1    Von Hacht, A.2    Hung, K.C.3    Dutton, R.J.4    Boyd, D.5    Bardwell, J.C.6    Ulmer, T.S.7
  • 45
    • 34247362408 scopus 로고    scopus 로고
    • Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
    • Malmstrom L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5:e76
    • (2007) PLoS Biol , vol.5 , pp. e76
    • Malmstrom, L.1    Riffle, M.2    Strauss, C.E.3    Chivian, D.4    Davis, T.N.5    Bonneau, R.6    Baker, D.7
  • 48
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of GenTHREADER method for genomic fold recognition
    • McGuffin L, Jones D (2003) Improvement of GenTHREADER method for genomic fold recognition. Bioinformatics 19:874-881
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • McGuffin, L.1    Jones, D.2
  • 50
    • 67349088738 scopus 로고    scopus 로고
    • Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
    • Michino M, Abola E, et al. (2009) Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov 8(6):455-463
    • (2009) Nat Rev Drug Discov , vol.8 , Issue.6 , pp. 455-463
    • Michino, M.1    Abola, E.2
  • 51
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S, Wunsch C (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48:443-453
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 57
    • 36749059956 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions in the high accuracy template-based modeling category
    • Read RJ, Chavali G (2007) Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 69(Suppl 8):27-37
    • (2007) Proteins , vol.69 , pp. 27-37
    • Read, R.J.1    Chavali, G.2
  • 59
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12:85-94
    • (1999) Protein Eng , vol.12 , pp. 85-94
    • Rost, B.1
  • 60
    • 84888679022 scopus 로고    scopus 로고
    • Large scale benchmarking of protein function prediction using modeled protein structures
    • Submitted
    • Roy A, Kucukural A, Mukherjee S, Hefty PS, Zhang Y (2010) Large scale benchmarking of protein function prediction using modeled protein structures. J Mol Biol (Submitted)
    • (2010) J Mol Biol
    • Roy, A.1    Kucukural, A.2    Mukherjee, S.3    Hefty, P.S.4    Zhang, Y.5
  • 61
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell T (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 63
    • 0031307019 scopus 로고    scopus 로고
    • Evaluation of comparative protein structure modelling by MODELLER-3
    • Sanchez R, Sali A (1997) Evaluation of comparative protein structure modelling by MODELLER-3. Proteins Suppl 1:50-58
    • (1997) Proteins Suppl , vol.1 , pp. 50-58
    • Sanchez, R.1    Sali, A.2
  • 64
    • 0032506030 scopus 로고    scopus 로고
    • Large scale structure modelling of the Saccharomyces cerevisiae genome
    • Sanchez R, Sali A (1998) Large scale structure modelling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci 95:13597-13602
    • (1998) Proc Natl Acad Sci , vol.95 , pp. 13597-13602
    • Sanchez, R.1    Sali, A.2
  • 66
    • 0027933763 scopus 로고
    • Locating ligand-binding sites in 7TM receptors by protein engineering
    • Schwartz TW (1994) Locating ligand-binding sites in 7TM receptors by protein engineering. Curr Opin Biotechnol 5:434-444
    • (1994) Curr Opin Biotechnol , vol.5 , pp. 434-444
    • Schwartz, T.W.1
  • 67
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J, Blundell TL, Mizuguchi K (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310:243-257
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 68
    • 0036169280 scopus 로고    scopus 로고
    • The binding site of aminergic G protein-coupled receptors: The transmembrane segments and second extracellular loop
    • Shi L, Javitch JA (2002) The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol 42:437-467
    • (2002) Annu Rev Pharmacol Toxicol , vol.42 , pp. 437-467
    • Shi, L.1    Javitch, J.A.2
  • 69
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268:209-225
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 70
    • 0035830958 scopus 로고    scopus 로고
    • Prospects for ab initio protein structural genomics
    • Simons KT, Strauss C, Baker D (2001) Prospects for ab initio protein structural genomics. J Mol Biol 306:1191-1199
    • (2001) J Mol Biol , vol.306 , pp. 1191-1199
    • Simons, K.T.1    Strauss, C.2    Baker, D.3
  • 71
    • 0026704815 scopus 로고
    • Detection of native like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations
    • Sippl M, Weitckus S (1992) Detection of native like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins 13:258-271
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.1    Weitckus, S.2
  • 72
    • 0034060287 scopus 로고    scopus 로고
    • Structural genomics and its importance for gene function analysis
    • Skolnick J, Fetrow JS, Kolinski A (2000) Structural genomics and its importance for gene function analysis. Nat Biotechnol 18:283-287
    • (2000) Nat Biotechnol , vol.18 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.S.2    Kolinski, A.3
  • 73
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
    • Skolnick J, Kihara D (2001) Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins: Struct Funct Genet 42:319-331
    • (2001) Proteins: Struct Funct Genet , vol.42 , pp. 319-331
    • Skolnick, J.1    Kihara, D.2
  • 74
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm
    • Skolnick J, Kihara D, Zhang Y (2004a) Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm. Proteins 56:502-518
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 75
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the Prospector-3 threading algorithm
    • Skolnick J, Kihara D, Zhang Y (2004b) Development and large scale benchmark testing of the Prospector-3 threading algorithm. Proteins 56:502-518
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 76
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195-197
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 77
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 78
    • 0242330730 scopus 로고    scopus 로고
    • Assesment of homology based predictions in CASP 5
    • Tramontano A, Morea V (2003) Assesment of homology based predictions in CASP 5. Proteins 53(Suppl 6):352-368
    • (2003) Proteins , vol.53 , pp. 352-368
    • Tramontano, A.1    Morea, V.2
  • 80
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases
    • Wallace AC, Laskowski RA, Thornton JM (1996) Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 5:1001-1013
    • (1996) Protein Sci , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 83
    • 0031720889 scopus 로고    scopus 로고
    • Genomics in the real world
    • Wiley SR (1998) Genomics in the real world. Curr Pharm Des 4:417-422
    • (1998) Curr Pharm des , vol.4 , pp. 417-422
    • Wiley, S.R.1
  • 84
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modelling of small proteins by iterative TASSER simulations
    • Wu S, Skolnick J, Zhang Y (2007a) Ab initio modelling of small proteins by iterative TASSER simulations. BMC Biol 5:17
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 85
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: A local meta-threading-server for protein structure prediction
    • Wu S, Zhang Y (2007b) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35(10):3375-3382
    • (2007) Nucleic Acids Res , vol.35 , Issue.10 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 86
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • Wu S, Zhang Y (2008a) A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 24:924-931
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 87
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu S, Zhang Y (2008b) MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72:547-556
    • (2008) Proteins , vol.72 , pp. 547-556
    • Wu, S.1    Zhang, Y.2
  • 89
    • 0034663738 scopus 로고    scopus 로고
    • Protein threading using PROSPECT: Design and evaluation
    • Xu Y, Xu D (2000) Protein threading using PROSPECT: design and evaluation. Proteins 40:343-354
    • (2000) Proteins , vol.40 , pp. 343-354
    • Xu, Y.1    Xu, D.2
  • 90
    • 0030627408 scopus 로고    scopus 로고
    • Similarities and differences between nonhomologous proteins with similar folds: Evaluation of threading strategies
    • Zhang B, Jaroszewski L, Rychlewski L, Godzik A (1997) Similarities and differences between nonhomologous proteins with similar folds: evaluation of threading strategies. Fold Des 2:307-317
    • (1997) Fold des , vol.2 , pp. 307-317
    • Zhang, B.1    Jaroszewski, L.2    Rychlewski, L.3    Godzik, A.4
  • 91
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8):108-117
    • (2007) Proteins , vol.69 , pp. 108-117
    • Zhang, Y.1
  • 92
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang Y (2008a) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40
    • (2008) BMC Bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 93
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Zhang Y (2008b) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18:342-348
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 94
    • 74249106219 scopus 로고    scopus 로고
    • I-TASSER: Fully automated protein structure prediction in CASP8
    • In press
    • Zhang Y (2009a) I-TASSER: fully automated protein structure prediction in CASP8. Proteins: In press
    • (2009) Proteins
    • Zhang, Y.1
  • 95
    • 64549115839 scopus 로고    scopus 로고
    • Protein structure prediction: When is it useful?
    • Zhang Y (2009b) Protein structure prediction: when is it useful? Curr Opin Struct Biol 19:145-155
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 145-155
    • Zhang, Y.1
  • 96
    • 33645793799 scopus 로고    scopus 로고
    • Structure modeling of all identified G protein-coupled receptors in the human genome
    • Zhang Y, Devries ME, Skolnick J (2006a) Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol 2:e13
    • (2006) PLoS Comput Biol , vol.2 , pp. e13
    • Zhang, Y.1    Devries, M.E.2    Skolnick, J.3
  • 98
    • 0036681386 scopus 로고    scopus 로고
    • Local energy landscape flattening: Parallel hyperbolic Monte-Carlo sampling of protein folding
    • Zhang Y, Kihara D, Skolnick J (2002) Local energy landscape flattening: Parallel hyperbolic Monte-Carlo sampling of protein folding. Proteins 48:192-201
    • (2002) Proteins , vol.48 , pp. 192-201
    • Zhang, Y.1    Kihara, D.2    Skolnick, J.3
  • 99
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85:1145-1164
    • (2003) Biophys J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 100
    • 2442676589 scopus 로고    scopus 로고
    • Automated Structure prediction of weekly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J (2004a) Automated Structure prediction of weekly homologous proteins on a genomic scale. Proc Natl Acad Sci 101:7594-7599
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 101
    • 1942519275 scopus 로고    scopus 로고
    • Spicker: Approach to clustering protein structures for near native model selection
    • Zhang Y, Skolnick J (2004b) Spicker: approach to clustering protein structures for near native model selection. J Comp Chem 25:865-871
    • (2004) J Comp Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 102
    • 16644386061 scopus 로고    scopus 로고
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
    • Zhang Y, Skolnick J (2004c) Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 87:2647-2655
    • (2004) Biophys J , vol.87 , pp. 2647-2655
    • Zhang, Y.1    Skolnick, J.2
  • 103
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang Y, Skolnick J (2005a) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102:1029-1034
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2
  • 104
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J (2005b) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33:2302-2309
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 105
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • Zhou H, Zhou Y (2004) Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 55:1005-1013
    • (2004) Proteins , vol.55 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 106
    • 11344292852 scopus 로고    scopus 로고
    • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
    • Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58:321-328
    • (2005) Proteins , vol.58 , pp. 321-328
    • Zhou, H.1    Zhou, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.