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Volumn 350, Issue , 2006, Pages 305-320

Thinking the impossible: How to solve the protein folding problem with and without homologous structures and more

Author keywords

3D modeling of globular proteins; 3D modeling of membrane proteins; Ab initio methods; Building by homology; Prediction of protein interacting patches; Protein folding; Protein structure prediction; Remote homologs; Threading; Validation

Indexed keywords

ALCOHOL DEHYDROGENASE; BETA3 INTEGRIN; GLOBULAR PROTEIN; MEMBRANE PROTEIN; PROTEIN GLUTAMINE GAMMA GLUTAMYLTRANSFERASE; VASOPRESSIN; PROTEIN;

EID: 39049189646     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1385/1-59745-189-4:305     Document Type: Article
Times cited : (10)

References (39)
  • 3
    • 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
  • 4
    • 0033764251 scopus 로고    scopus 로고
    • Protein structure modeling for structural genomics
    • Sanchez, R., Pieper, U., Melo, F., et al. (2000) Protein structure modeling for structural genomics. Nat. Struct. Biol. 7 Suppl, 986-990.
    • (2000) Nat. Struct. Biol , vol.7 , pp. 986-990
    • Sanchez, R.1    Pieper, U.2    Melo, F.3
  • 5
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • Moult, J. (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 15, 285-289.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 285-289
    • Moult, J.1
  • 6
    • 0037263887 scopus 로고    scopus 로고
    • CASP and CAFASP experiments and their findings. Methods Biochem
    • Bourne, P. E. (2003) CASP and CAFASP experiments and their findings. Methods Biochem. Anal. 44, 501-507.
    • (2003) Anal , vol.44 , pp. 501-507
    • Bourne, P.E.1
  • 7
    • 0036968925 scopus 로고    scopus 로고
    • De novo prediction of threedimensional structures for major protein families
    • Bonneau, R., Strauss, C. E., Rohl, C. A., et al. (2002) De novo prediction of threedimensional structures for major protein families. J. Mol. Biol. 322, 65-78.
    • (2002) J. Mol. Biol , vol.322 , pp. 65-78
    • Bonneau, R.1    Strauss, C.E.2    Rohl, C.A.3
  • 8
    • 2942576133 scopus 로고    scopus 로고
    • The interplay of fold recognition and experimental structure determination in structural genomics
    • Friedberg, I., Jaroszewski, L. Y., and Godzik, A. (2004) The interplay of fold recognition and experimental structure determination in structural genomics. Curr. Opin. Struct. Biol. 14, 307-312.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 307-312
    • Friedberg, I.1    Jaroszewski, L.Y.2    Godzik, A.3
  • 9
    • 0347719520 scopus 로고    scopus 로고
    • A Shannon entropybased filter detects high-quality profile-profile alignments in searches for remote homologues
    • Capriotti, E., Fariselli, P., Rossi, I., and Casadio, R. (2004) A Shannon entropybased filter detects high-quality profile-profile alignments in searches for remote homologues. Proteins 54, 351-360.
    • (2004) Proteins , vol.54 , pp. 351-360
    • Capriotti, E.1    Fariselli, P.2    Rossi, I.3    Casadio, R.4
  • 10
    • 3442901082 scopus 로고    scopus 로고
    • Improving fold recognition without folds
    • Prybylski, D. and Rost B. (2004) Improving fold recognition without folds. J. Mol. Biol. 341, 255-269.
    • (2004) J. Mol. Biol , vol.341 , pp. 255-269
    • Prybylski, D.1    Rost, B.2
  • 12
    • 0034595501 scopus 로고    scopus 로고
    • Enhanced genome annotation using structural profiles in the program 3D-PSSM
    • Kelley, L. A., McCallum, R. M., and Sternberg, M. J. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-520.
    • (2000) J. Mol. Biol , vol.299 , pp. 499-520
    • Kelley, L.A.1    McCallum, R.M.2    Sternberg, M.J.3
  • 13
    • 0029186289 scopus 로고
    • TOPITS: Threading one-dimensional predictions into threedimensional structures
    • Rost, B. (1995) TOPITS: threading one-dimensional predictions into threedimensional structures. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 314-321.
    • (1995) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.3 , pp. 314-321
    • Rost, B.1
  • 14
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the GenTHREADER method for genomic fold recognition
    • Mc Guffin, L. J. and Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19, 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • Mc Guffin, L.J.1    Jones, D.T.2
  • 15
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition metapredictor
    • Fischer, D. (2003) 3D-SHOTGUN: a novel, cooperative, fold-recognition metapredictor. Proteins 51, 434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 16
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A. and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-781.
    • (1993) J. Mol. Biol , vol.234 , pp. 779-781
    • Sali, A.1    Blundell, T.L.2
  • 17
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
    • (1993) J. Appl. Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 18
    • 0027490731 scopus 로고
    • Recognition of errors in three-dimensional structures of proteins
    • Sippl, M. J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
    • (1993) Proteins , vol.17 , pp. 355-362
    • Sippl, M.J.1
  • 19
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modeling and drug design program
    • Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52-56.
    • (1990) J. Mol. Graph , vol.8 , pp. 52-56
    • Vriend, G.1
  • 20
    • 4143066779 scopus 로고    scopus 로고
    • In silico prediction of the structure of membrane proteins: Is it feasible?
    • Casadio, R., Fariselli, P., and Martelli, P. L. (2003) In silico prediction of the structure of membrane proteins: is it feasible? Brief Bioinf. 4, 341-348.
    • (2003) Brief Bioinf , vol.4 , pp. 341-348
    • Casadio, R.1    Fariselli, P.2    Martelli, P.L.3
  • 21
    • 0037024368 scopus 로고    scopus 로고
    • A 3D model of the voltage-dependent anion channel
    • Casadio, R., Jacoboni, I., Messina, A., and De Pinto, V. (2002) A 3D model of the voltage-dependent anion channel. FEBS Lett. 520, 1-7.
    • (2002) FEBS Lett , vol.520 , pp. 1-7
    • Casadio, R.1    Jacoboni, I.2    Messina, A.3    De Pinto, V.4
  • 22
    • 2942532202 scopus 로고    scopus 로고
    • Functional characterization of a second porin isoform in drosophila melanogster: DmPorin2 forms voltage-independent cation selective pores
    • Aiello, R., Messina, A., Schiffler, B., et al. (2004) Functional characterization of a second porin isoform in drosophila melanogster: DmPorin2 forms voltage-independent cation selective pores. J. Biol. Chem. 279, 25,364-25,373.
    • (2004) J. Biol. Chem , vol.279 , Issue.25
    • Aiello, R.1    Messina, A.2    Schiffler, B.3
  • 23
    • 28544449567 scopus 로고    scopus 로고
    • Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: A spectroscopic and molecular modelling study
    • Morozzo della Rocca, B., Miniero, D. V., Tasco, G., et al. (2005) Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study. Mol. Membr. Biol. 22, 443-445.
    • (2005) Mol. Membr. Biol , vol.22 , pp. 443-445
    • Morozzo Della Rocca, B.1    Miniero, D.V.2    Tasco, G.3
  • 24
    • 0036583445 scopus 로고    scopus 로고
    • Protein structure prediction and biomolecular recognition: From protein sequence to peptidomimetic design with the human beta 3 integrin SAR QSAR
    • Casadio, R., Compiani, M., Facchiano, A., et al. (2002) Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta 3 integrin SAR QSAR Envir Res 13, 473-486.
    • (2002) Envir Res , vol.13 , pp. 473-486
    • Casadio, R.1    Compiani, M.2    Facchiano, A.3
  • 25
    • 0001050957 scopus 로고    scopus 로고
    • The structural basis for the regulation of tissue transglutaminase by calcium ions
    • Casadio, R., Polverini, E., Mariani, P., et al. (1999) The structural basis for the regulation of tissue transglutaminase by calcium ions. Eur. J. Biochem. 262, 672-679.
    • (1999) Eur. J. Biochem , vol.262 , pp. 672-679
    • Casadio, R.1    Polverini, E.2    Mariani, P.3
  • 26
    • 23244448567 scopus 로고    scopus 로고
    • Histone deacetylase 1: A target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer
    • Calonghi, N., Cappadone, C., Pagnotta, E., et al. (2005) Histone deacetylase 1: a target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer. J. Lipid Res. 46, 1569-1603.
    • (2005) J. Lipid Res , vol.46 , pp. 1569-1603
    • Calonghi, N.1    Cappadone, C.2    Pagnotta, E.3
  • 27
    • 0036094261 scopus 로고    scopus 로고
    • Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the Herpes Simplex virus gD binding site confers high-affinity binding to gD
    • Menotti, L., Casadio, R., Bertucci, C., Lopez, M., and Campadelli-Fiume, G. (2002) Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the Herpes Simplex virus gD binding site confers high-affinity binding to gD. J. Virol. 76, 5463-5471.
    • (2002) J. Virol , vol.76 , pp. 5463-5471
    • Menotti, L.1    Casadio, R.2    Bertucci, C.3    Lopez, M.4    Campadelli-Fiume, G.5
  • 28
    • 0036230272 scopus 로고    scopus 로고
    • A lowresolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus
    • Casadio, R., Martelli, P. L., Giordano, A., Rossi, M., and Raia, C. A. (2002) A lowresolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus. Protein Eng. 15, 215-223.
    • (2002) Protein Eng , vol.15 , pp. 215-223
    • Casadio, R.1    Martelli, P.L.2    Giordano, A.3    Rossi, M.4    Raia, C.A.5
  • 29
    • 12444253048 scopus 로고    scopus 로고
    • 3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering
    • Occhipinti, E., Martelli, P. L., Spinozzi, F., et al. (2003) 3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering. Biophys. J. 85, 1165-1175.
    • (2003) Biophys. J , vol.85 , pp. 1165-1175
    • Occhipinti, E.1    Martelli, P.L.2    Spinozzi, F.3
  • 30
    • 0037023363 scopus 로고    scopus 로고
    • Crystal structure of the extracellular segment of Integrin alpha V-beta3 in complex with an Arg-Gly-Asp ligand
    • Xiong, J. P., Stehle, T., Zhang, R., et al. (2002) Crystal structure of the extracellular segment of Integrin alpha V-beta3 in complex with an Arg-Gly-Asp ligand. Science 296, 151-155.
    • (2002) Science , vol.296 , pp. 151-155
    • Xiong, J.P.1    Stehle, T.2    Zhang, R.3
  • 31
    • 0037022619 scopus 로고    scopus 로고
    • Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity
    • Liu, S., Ceriona, R. A., and Clardy, J. (2002) Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity. Proc. Natl. Acad. Sci. USA 99, 2743–2747.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 2743-2747
    • Liu, S.1    Ceriona, R.A.2    Clardy, J.3
  • 32
    • 0036301867 scopus 로고    scopus 로고
    • Crystal structure of alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus Solfataricus at 1.85 Angstrom resolution
    • Esposito, L., Sica, F., Raia, C. A., et al. (2002) Crystal structure of alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus Solfataricus at 1.85 Angstrom resolution J. Mol. Biol. 318, 463–477.
    • (2002) J. Mol. Biol , vol.318 , pp. 463-477
    • Esposito, L.1    Sica, F.2    Raia, C.A.3
  • 33
    • 13844255392 scopus 로고    scopus 로고
    • Protein complexes: Structure prediction challenges for the 21st century
    • Aloy, P., Pichaut, M., and Russel, R. B. (2005) Protein complexes: structure prediction challenges for the 21st century. Curr. Opin. Struct. Biol. 15, 15–22.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 15-22
    • Aloy, P.1    Pichaut, M.2    Russel, R.B.3
  • 34
    • 0036122073 scopus 로고    scopus 로고
    • Prediction of protein–protein interaction sites in heterocomplexes with neural networks
    • Fariselli, P., Pazos, F., Valencia, A., and Casadio, R. (2002) Prediction of protein–protein interaction sites in heterocomplexes with neural networks. Eur. J. Biochem. 269, 1356–1361.
    • (2002) Eur. J. Biochem. , vol.269 , pp. 1356-1361
    • Fariselli, P.1    Pazos, F.2    Valencia, A.3    Casadio, R.4
  • 36
    • 0034563423 scopus 로고    scopus 로고
    • Predictions of protein segments with the same aminoacid sequence and different secondary structure: A benchmark for predictive methods
    • Jacoboni, I., Martelli, P. L., Fariselli, P., Compiani, M., and Casadio, R. (2000) Predictions of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods. Proteins 41, 535–544.
    • (2000) Proteins , vol.41 , pp. 535-544
    • Jacoboni, I.1    Martelli, P.L.2    Fariselli, P.3    Compiani, M.4    Casadio, R.5
  • 37
    • 0036937367 scopus 로고    scopus 로고
    • Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks
    • Martelli, P. L., Fariselli, P., Malaguti, L., and Casadio, R. (2002) Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. Protein Eng. 15, 951–953.
    • (2002) Protein Eng , vol.15 , pp. 951-953
    • Martelli, P.L.1    Fariselli, P.2    Malaguti, L.3    Casadio, R.4
  • 38
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 39
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I. N. and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11, 739–747.
    • (1998) Protein Eng , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2


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