메뉴 건너뛰기




Volumn 293, Issue 5, 1999, Pages 1221-1239

Effective use of sequence correlation and conservation in fold recognition

Author keywords

Conservation; Contact prediction; Correlation; Incorrectly folded models; Threading

Indexed keywords

ARTICLE; CORRELATION FUNCTION; GENETIC CONSERVATION; GENETIC PROCEDURES; MOLECULAR RECOGNITION; MUTATION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

EID: 0033550256     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3208     Document Type: Article
Times cited : (154)

References (89)
  • 1
    • 84986522918 scopus 로고
    • ICM-a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R., Totrov M., Kuznetsov D. ICM-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15:1994;488-506.
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 2
    • 0023660022 scopus 로고
    • Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh D., Lesk A. M., Bloomer A. C., Klug A. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol. 193:1987;693-707.
    • (1987) J. Mol. Biol. , vol.193 , pp. 693-707
    • Altschuh, D.1    Lesk, A.M.2    Bloomer, A.C.3    Klug, A.4
  • 3
    • 0024084164 scopus 로고
    • Coordinated amino acid changes in homologous protein families
    • Altschuh D., Vernet T., Moras D., Nagai K. Coordinated amino acid changes in homologous protein families. Protein Eng. 2:1988;193-199.
    • (1988) Protein Eng. , vol.2 , pp. 193-199
    • Altschuh, D.1    Vernet, T.2    Moras, D.3    Nagai, K.4
  • 4
    • 0031157904 scopus 로고    scopus 로고
    • Classification of protein families and detection of the determinant residues with an improved self-organizing map
    • Andrade M. A., Casari G., Sander C., Valencia A. Classification of protein families and detection of the determinant residues with an improved self-organizing map. Biol. Cybern. 76:1997;441-450.
    • (1997) Biol. Cybern. , vol.76 , pp. 441-450
    • Andrade, M.A.1    Casari, G.2    Sander, C.3    Valencia, A.4
  • 5
    • 0027221842 scopus 로고
    • Three-dimensional structural resemblance between the ribonuclease H and connection domain of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques
    • Artymiuk P. J., Grindley H. M., Kumar K., Rice D. W., Willett D. W. Three-dimensional structural resemblance between the ribonuclease H and connection domain of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques. FEBS Letters. 324:1993;15-21.
    • (1993) FEBS Letters , vol.324 , pp. 15-21
    • Artymiuk, P.J.1    Grindley, H.M.2    Kumar, K.3    Rice, D.W.4    Willett, D.W.5
  • 6
    • 0026553672 scopus 로고
    • PROSITE: A dictionary of sites and patterns in proteins
    • Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucl. Acids Res. 20:1992;2013-2018.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 2013-2018
    • Bairoch, A.1
  • 7
    • 0024839793 scopus 로고
    • Patterns of divergence in homologous proteins as indicators of tertiary and quaternary structure
    • Benner S. A. Patterns of divergence in homologous proteins as indicators of tertiary and quaternary structure. Advan. Enzyme Regul. 28:1989;219-236.
    • (1989) Advan. Enzyme Regul. , vol.28 , pp. 219-236
    • Benner, S.A.1
  • 8
    • 0025935158 scopus 로고
    • Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: A prediction of the structure of the catalytic domain of protein kinases
    • Benner S. A., Gerloff D. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure of the catalytic domain of protein kinases. Advan. Enzyme Regul. 31:1991;121-181.
    • (1991) Advan. Enzyme Regul. , vol.31 , pp. 121-181
    • Benner, S.A.1    Gerloff, D.2
  • 9
    • 0024977234 scopus 로고
    • Recognition of functional regions in primary structures using a set of property patterns
    • Bork P. Recognition of functional regions in primary structures using a set of property patterns. FEBS Letters. 257:1989;191-195.
    • (1989) FEBS Letters , vol.257 , pp. 191-195
    • Bork, P.1
  • 10
    • 0028955737 scopus 로고
    • Divergent evolution of a b/a barrel subclass: Detection of numerous phosphate-binding sites by motif search
    • Bork P., Gellerich J., Groth H., Hooft R., Martin F. Divergent evolution of a b/a barrel subclass: detection of numerous phosphate-binding sites by motif search. Protein Sci. 4:1995;268-274.
    • (1995) Protein Sci. , vol.4 , pp. 268-274
    • Bork, P.1    Gellerich, J.2    Groth, H.3    Hooft, R.4    Martin, F.5
  • 11
    • 0025341237 scopus 로고
    • Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
    • Bowie D., Clarke N. D., Pabo C. O., Sauer R. T. Identification of protein folds: matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins: Struct. Funct. Genet. 7:1990;257-264.
    • (1990) Proteins: Struct. Funct. Genet. , vol.7 , pp. 257-264
    • Bowie, D.1    Clarke, N.D.2    Pabo, C.O.3    Sauer, R.T.4
  • 12
    • 0023078443 scopus 로고
    • Correctly folded proteins make twice as many hydrophobic contacts
    • Bryant S. H., Amzel L. M. Correctly folded proteins make twice as many hydrophobic contacts. J. Int. Pept. Protein Res. 29:1987;46-52.
    • (1987) J. Int. Pept. Protein Res. , vol.29 , pp. 46-52
    • Bryant, S.H.1    Amzel, L.M.2
  • 13
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • Casari G., Sander C., Valencia A. A method to predict functional residues in proteins. Nature Struct. Biol. 2:1995;171-178.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 15
    • 0026052571 scopus 로고
    • Protein topology prediction through constraint-based search and the evaluation of topological folding rules
    • Clark D. A., Shirazi J., Rawlings C. J. Protein topology prediction through constraint-based search and the evaluation of topological folding rules. Protein Eng. 4:1991;751-760.
    • (1991) Protein Eng. , vol.4 , pp. 751-760
    • Clark, D.A.1    Shirazi, J.2    Rawlings, C.J.3
  • 16
    • 0026628087 scopus 로고
    • Evolutionary conservation of the active site of soluble inorganic pyrophosphatase
    • Cooperman B. S., Baykov A. A., Lahti R. Evolutionary conservation of the active site of soluble inorganic pyrophosphatase. Trends Biochem. Sci. 17:1992;262-266.
    • (1992) Trends Biochem. Sci. , vol.17 , pp. 262-266
    • Cooperman, B.S.1    Baykov, A.A.2    Lahti, R.3
  • 17
    • 0030595366 scopus 로고    scopus 로고
    • Multiple sequence information for threading algorithms
    • Defay T. R., Cohen F. E. Multiple sequence information for threading algorithms. J . Mol. Biol. 262:1996;314-323.
    • (1996) J . Mol. Biol. , vol.262 , pp. 314-323
    • Defay, T.R.1    Cohen, F.E.2
  • 18
    • 0033047710 scopus 로고    scopus 로고
    • A neural network based predictor of residue contacts in proteins
    • Fariselli P., Casadio R. A neural network based predictor of residue contacts in proteins. Protein Eng. 12:1999;15-21.
    • (1999) Protein Eng. , vol.12 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 19
    • 0029874551 scopus 로고    scopus 로고
    • Protein fold recognition using sequence-derived predictions
    • Fisher D., Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955.
    • (1996) Protein Sci. , vol.5 , pp. 947-955
    • Fisher, D.1    Eisenberg, D.2
  • 20
    • 0025308572 scopus 로고
    • On searching for the active sites in proteins and peptide hormones
    • Gabrielian A. E., Ivanov V. S., Kozhich A. T. On searching for the active sites in proteins and peptide hormones. Comput. Appl. Biosci. 6:1990;1-2.
    • (1990) Comput. Appl. Biosci. , vol.6 , pp. 1-2
    • Gabrielian, A.E.1    Ivanov, V.S.2    Kozhich, A.T.3
  • 21
    • 0028933342 scopus 로고
    • Properties of intraglobular contacts in proteins: An approach to prediction of tertiary structure
    • H. L. Waileas. IEEE Society Press
    • Galaktionov S. G., Marshall G. R. Properties of intraglobular contacts in proteins: An approach to prediction of tertiary structure. Waileas H. L. 27th Hawaii International Conference on System Sciences. 1994;326-335 IEEE Society Press.
    • (1994) 27th Hawaii International Conference on System Sciences , pp. 326-335
    • Galaktionov, S.G.1    Marshall, G.R.2
  • 22
    • 0004009893 scopus 로고
    • Calculation of the tertiary structure of proteins on the basis of analysis of the matrices of contacts between amino acid residues
    • Galaktionov S. G., Rodionov M. A. Calculation of the tertiary structure of proteins on the basis of analysis of the matrices of contacts between amino acid residues. Biophysics. 25:1981;395-403.
    • (1981) Biophysics , vol.25 , pp. 395-403
    • Galaktionov, S.G.1    Rodionov, M.A.2
  • 24
    • 0024373407 scopus 로고
    • Conservation of residue interactions in a family of Ca-binding proteins
    • Godzik A., Sander C. Conservation of residue interactions in a family of Ca-binding proteins. Protein Eng. 2:1989;589-596.
    • (1989) Protein Eng. , vol.2 , pp. 589-596
    • Godzik, A.1    Sander, C.2
  • 25
    • 0025269891 scopus 로고
    • Novel method for the rapid evaluation of packing in protein structures
    • Gregoret L. M., Cohen F. E. Novel method for the rapid evaluation of packing in protein structures. J. Mol. Biol. 211:1990;959-974.
    • (1990) J. Mol. Biol. , vol.211 , pp. 959-974
    • Gregoret, L.M.1    Cohen, F.E.2
  • 27
    • 0025008445 scopus 로고
    • Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
    • Hendlich M., Lackner P., Weitckus S., Floeckner H., Froschauer R., Gottsbacher K., Casari G., Sippl M. J. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216:1990;167-180.
    • (1990) J. Mol. Biol. , vol.216 , pp. 167-180
    • Hendlich, M.1    Lackner, P.2    Weitckus, S.3    Floeckner, H.4    Froschauer, R.5    Gottsbacher, K.6    Casari, G.7    Sippl, M.J.8
  • 29
    • 0026505184 scopus 로고
    • Evaluation of protein models by atomic solvation preference
    • Holm L., Sander C. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225:1992;93-105.
    • (1992) J. Mol. Biol. , vol.225 , pp. 93-105
    • Holm, L.1    Sander, C.2
  • 30
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 31
    • 0028232955 scopus 로고
    • Searching protein structure databases has come of age
    • Holm L., Sander C. Searching protein structure databases has come of age. Proteins: Struct. Funct. Genet. 19:1994;165-173.
    • (1994) Proteins: Struct. Funct. Genet. , vol.19 , pp. 165-173
    • Holm, L.1    Sander, C.2
  • 32
    • 0029360327 scopus 로고
    • DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily
    • Holm L., Sander C. DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem. Sci. 20:1995;45-347.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 45-347
    • Holm, L.1    Sander, C.2
  • 33
    • 0029918694 scopus 로고    scopus 로고
    • The FSSP database: Fold classification based on structure-structure alignment of proteins
    • Holm L., Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucl. Acids Res. 24:1996;206-210.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 206-210
    • Holm, L.1    Sander, C.2
  • 35
    • 0024318517 scopus 로고
    • Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis
    • Howell N. Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis. J. Mol. Evol. 29:1989;157-169.
    • (1989) J. Mol. Evol. , vol.29 , pp. 157-169
    • Howell, N.1
  • 36
    • 0029101826 scopus 로고
    • Recognizing native folds by the arrangament of hydrophobic and polar residues
    • Huang E. S., Subbiah S., Levitt M. Recognizing native folds by the arrangament of hydrophobic and polar residues. J. Mol. Biol. 252:1995;709-720.
    • (1995) J. Mol. Biol. , vol.252 , pp. 709-720
    • Huang, E.S.1    Subbiah, S.2    Levitt, M.3
  • 37
    • 0029871791 scopus 로고    scopus 로고
    • Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular simulations
    • Huang E. S., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular simulations. J. Mol. Biol. 257:1996;716-725.
    • (1996) J. Mol. Biol. , vol.257 , pp. 716-725
    • Huang, E.S.1    Subbiah, S.2    Tsai, J.3    Levitt, M.4
  • 38
    • 0000338489 scopus 로고
    • Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard T. J. L., Blundell T. L. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1:1987;159-171.
    • (1987) Protein Eng. , vol.1 , pp. 159-171
    • Hubbard, T.J.L.1    Blundell, T.L.2
  • 39
    • 0028874810 scopus 로고
    • Fold recognition and ab initio structure predictions using hidden Markov models and β-strand pair potentials
    • Hubbard T. J., Park J. Fold recognition and ab initio structure predictions using hidden Markov models and β-strand pair potentials. Proteins: Struct. Funct. Genet. 23:1995;398-402.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 398-402
    • Hubbard, T.J.1    Park, J.2
  • 40
    • 0022541494 scopus 로고
    • Convergent and divergent evolution of regulatory sites in eukaryotic phosphorylases
    • Hwang P. K., Fletterick R. J. Convergent and divergent evolution of regulatory sites in eukaryotic phosphorylases. Nature. 234:1986;80-83.
    • (1986) Nature , vol.234 , pp. 80-83
    • Hwang, P.K.1    Fletterick, R.J.2
  • 41
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 42
    • 0028818570 scopus 로고
    • Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
    • Juffer A. H., Eisenhaber F., Hubbard S. J., Walther D., Argos P. Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding. Protein Sci. 4:1995;2499-2509.
    • (1995) Protein Sci. , vol.4 , pp. 2499-2509
    • Juffer, A.H.1    Eisenhaber, F.2    Hubbard, S.J.3    Walther, D.4    Argos, P.5
  • 43
    • 0029886749 scopus 로고    scopus 로고
    • Protein sequence comparison at genome scale
    • Koonin E. V., Tatusov R. L., Rudd K. E. Protein sequence comparison at genome scale. Methods Enzymol. 266:1996;295-322.
    • (1996) Methods Enzymol. , vol.266 , pp. 295-322
    • Koonin, E.V.1    Tatusov, R.L.2    Rudd, K.E.3
  • 45
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O., Bourne H. R., Cohen F. E. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:1996;342-358.
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 46
    • 0027764344 scopus 로고
    • Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
    • Livingstone C. D., Barton G. J. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci. 6:1993;645-756.
    • (1993) Comput. Appl. Biosci. , vol.6 , pp. 645-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 47
    • 0031406438 scopus 로고    scopus 로고
    • Protein distance constraints predicted by neural networks and probability density functions
    • Lund O., Frimand K., Gorodkin J., Bohr H., Bohr J., Hansen J., Brunak S. Protein distance constraints predicted by neural networks and probability density functions. Protein Eng. 10:1997;1241-1248.
    • (1997) Protein Eng. , vol.10 , pp. 1241-1248
    • Lund, O.1    Frimand, K.2    Gorodkin, J.3    Bohr, H.4    Bohr, J.5    Hansen, J.6    Brunak, S.7
  • 48
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Lüthy R., Bowie J. U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 356:1992;83-85.
    • (1992) Nature , vol.356 , pp. 83-85
    • Lüthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 49
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov V. N., Crippen G. M. Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227:1992;876-888.
    • (1992) J. Mol. Biol. , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 50
    • 0027050193 scopus 로고
    • Structural homology between rbs repressor and ribose binding protein implies functional similarity
    • Mauzy C. A., Hermodson M. A. Structural homology between rbs repressor and ribose binding protein implies functional similarity. Protein Sci. 1:1992;843-849.
    • (1992) Protein Sci. , vol.1 , pp. 843-849
    • Mauzy, C.A.1    Hermodson, M.A.2
  • 51
    • 0015243774 scopus 로고
    • Test for comparing related amino acid sequences
    • Mclachlan A. D. Test for comparing related amino acid sequences. J. Mol. Biol. 61:1971;409-424.
    • (1971) J. Mol. Biol. , vol.61 , pp. 409-424
    • Mclachlan, A.D.1
  • 52
    • 0029950031 scopus 로고    scopus 로고
    • Structural classification of proteins: New superfamilies
    • Murzin A. G. Structural classification of proteins: new superfamilies. Curr. Opin. Struct. Biol. 6:1996;386-394.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 386-394
    • Murzin, A.G.1
  • 53
    • 0028125904 scopus 로고
    • How frequent are correlated changes in families of protein sequences?
    • Neher E. How frequent are correlated changes in families of protein sequences? Proc. Natl Acad. Sci. USA. 91:1994;98-102.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 98-102
    • Neher, E.1
  • 54
    • 0021691918 scopus 로고
    • An analysis of incorrectly folded models. Implications for structure prediction
    • Novotny J., Bruccoleri R. E., Karplus M. An analysis of incorrectly folded models. Implications for structure prediction. J. Mol. Biol. 177:1984;787-818.
    • (1984) J. Mol. Biol. , vol.177 , pp. 787-818
    • Novotny, J.1    Bruccoleri, R.E.2    Karplus, M.3
  • 55
    • 0023804632 scopus 로고
    • Criteria that discriminate between native proteins and incorrectly folded models
    • Novotny J., Rashin A. A., Bruccoleri R. E. Criteria that discriminate between native proteins and incorrectly folded models. Proteins: Struct. Funct. Genet. 4:1988;19-30.
    • (1988) Proteins: Struct. Funct. Genet. , vol.4 , pp. 19-30
    • Novotny, J.1    Rashin, A.A.2    Bruccoleri, R.E.3
  • 56
    • 0030627941 scopus 로고    scopus 로고
    • Improving contact predictions by the combination of correlated mutations and other sources of sequence information
    • Olmea O., Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold. Des. 2:1997;S25-S32.
    • (1997) Fold. Des. , vol.2
    • Olmea, O.1    Valencia, A.2
  • 57
    • 0032571390 scopus 로고    scopus 로고
    • Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments
    • Ortiz A. R., Kolinski A., Skolnick J. Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. J. Mol. Biol. 277:1998a;419-448.
    • (1998) J. Mol. Biol. , vol.277 , pp. 419-448
    • Ortiz, A.R.1    Kolinski, A.2    Skolnick, J.3
  • 58
    • 0032477713 scopus 로고    scopus 로고
    • Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations
    • Ortiz A. R., Kolinski A., Skolnick J. Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. Proc. Natl Acad. Sci. USA. 95:1998b;1020-1025.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1020-1025
    • Ortiz, A.R.1    Kolinski, A.2    Skolnick, J.3
  • 59
    • 0027302043 scopus 로고
    • Prediction of protein structure by evaluation of sequence-structure fitness: Aligning sequences to contact profiles derived from three-dimensional structures
    • Ouzounis C., Sander C., Scharf M., Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol. 232:1993;805-825.
    • (1993) J. Mol. Biol. , vol.232 , pp. 805-825
    • Ouzounis, C.1    Sander, C.2    Scharf, M.3    Schneider, R.4
  • 61
    • 0025026058 scopus 로고
    • Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship
    • Pastore A., Lesk A. M. Comparison of the structures of globins and phycocyanins: evidence for evolutionary relationship. Proteins: Struct. Funct. Genet. 8:1990;133-155.
    • (1990) Proteins: Struct. Funct. Genet. , vol.8 , pp. 133-155
    • Pastore, A.1    Lesk, A.M.2
  • 62
    • 0000971646 scopus 로고    scopus 로고
    • Correlated mutations contain information about protein-protein interaction
    • Pazos F., Helmer-Citterich M., Ausiello G., Valencia A. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 272:1997a;1-13.
    • (1997) J. Mol. Biol. , vol.272 , pp. 1-13
    • Pazos, F.1    Helmer-Citterich, M.2    Ausiello, G.3    Valencia, A.4
  • 63
    • 0030927252 scopus 로고    scopus 로고
    • A graphical interface for correlated mutations and other structure prediction methods
    • Pazos F., Olmea O., Valencia A. A graphical interface for correlated mutations and other structure prediction methods. Comput. Appl. Biosci. 13:1997b;319-321.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 319-321
    • Pazos, F.1    Olmea, O.2    Valencia, A.3
  • 64
    • 0002832714 scopus 로고    scopus 로고
    • Comparative analysis of different methods for the detection of specificity regions in protein families
    • Lund D. et al. New Jersey, London: World Scientific, Singapore
    • Pazos F., Sanchez-Pulido L., García-Ranea J. A., Andrade M. A., Atrian S., Valencia A. Comparative analysis of different methods for the detection of specificity regions in protein families. Lund D. et al. Biocomputing and Emergent Computation. 1997c;132-145 World Scientific, Singapore, New Jersey, London.
    • (1997) Biocomputing and Emergent Computation , pp. 132-145
    • Pazos, F.1    Sanchez-Pulido, L.2    García-Ranea, J.A.3    Andrade, M.A.4    Atrian, S.5    Valencia, A.6
  • 65
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • Pollock D. D., Taylor W. R. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10:1997;647-657.
    • (1997) Protein Eng. , vol.10 , pp. 647-657
    • Pollock, D.D.1    Taylor, W.R.2
  • 66
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock D. D., Taylor W. R., Goldman N. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 287:1999;187-198.
    • (1999) J. Mol. Biol. , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 67
    • 0026458189 scopus 로고
    • Extracting information on folding from the amino acid sequence: Consensus regions with preferred conformation in homologous proteins
    • Rooman M. J., Wodak S. J. Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. Biochemistry. 31:1992;10239-10249.
    • (1992) Biochemistry , vol.31 , pp. 10239-10249
    • Rooman, M.J.1    Wodak, S.J.2
  • 68
    • 0026447086 scopus 로고
    • Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactons
    • Rooman M. J., Kocher J.-P. A., Wodak S. J. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactons. Biochemistry. 31:1992;10226-10238.
    • (1992) Biochemistry , vol.31 , pp. 10226-10238
    • Rooman, M.J.1    Kocher, J.-P.A.2    Wodak, S.J.3
  • 69
    • 0029186289 scopus 로고
    • TOPITS: Threading one-dimensional predictions into three-dimensional structures
    • C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer, & S. Wodak. Cambridge: AAAI PressMenlo Park, CA
    • Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structures. Rawlings C., Clark D., Altman R., Hunter L., Lengauer T., Wodak S. Third International Conference on Intelligent Systems for Molecular Biology. 1995;314-321 AAAI PressMenlo Park, CA, Cambridge.
    • (1995) Third International Conference on Intelligent Systems for Molecular Biology , pp. 314-321
    • Rost, B.1
  • 70
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B., Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Funct. Genet. 20:1994;216-226.
    • (1994) Proteins: Struct. Funct. Genet. , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 71
    • 0031577260 scopus 로고    scopus 로고
    • Protein fold recognition by prediction-based threading
    • Rost B., Schneider R., Sander C. Protein fold recognition by prediction-based threading. J. Mol. Biol. 270:1997;471-480.
    • (1997) J. Mol. Biol. , vol.270 , pp. 471-480
    • Rost, B.1    Schneider, R.2    Sander, C.3
  • 72
    • 0027288463 scopus 로고
    • The HSSP data base of protein structure-sequence alignments
    • Sander C., Schneider R. The HSSP data base of protein structure-sequence alignments. Nucl. Acids Res. 21:1993;3105-3109.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3105-3109
    • Sander, C.1    Schneider, R.2
  • 73
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations
    • Shindyalov I. N., Kolchanov N. A., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations. Protein Eng. 7:1994;349-358.
    • (1994) Protein Eng. , vol.7 , pp. 349-358
    • Shindyalov, I.N.1    Kolchanov, N.A.2    Sander, C.3
  • 74
    • 0029164276 scopus 로고
    • Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis
    • Singer M. S., Oliveira L., Vriend G., Shepherd G. M. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis. Recept. Chann. 3:1995;89-95.
    • (1995) Recept. Chann. , vol.3 , pp. 89-95
    • Singer, M.S.1    Oliveira, L.2    Vriend, G.3    Shepherd, G.M.4
  • 75
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl M. J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5:1995;229-235.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 76
    • 0026704815 scopus 로고
    • Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
    • Sippl M. J., Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins: Struct. Funct. Genet. 13:1992;258-271.
    • (1992) Proteins: Struct. Funct. Genet. , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 77
    • 0026527758 scopus 로고
    • Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
    • Smith R. F., Smith T. F. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling. Protein Eng. 5:1992;35-41.
    • (1992) Protein Eng. , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 78
    • 0028097046 scopus 로고
    • Trifluoroethanol stabilizes a helix-turn-helix motif in equine infectious-anemina-virus trans-activator protein
    • Sticht H., Willbold D., Ejchart A., Rosin-Arbesfeld R., Yaniv A., Gazit A., Rösch P. Trifluoroethanol stabilizes a helix-turn-helix motif in equine infectious-anemina-virus trans-activator protein. Eur. J. Biochem. 225:1994;855-861.
    • (1994) Eur. J. Biochem. , vol.225 , pp. 855-861
    • Sticht, H.1    Willbold, D.2    Ejchart, A.3    Rosin-Arbesfeld, R.4    Yaniv, A.5    Gazit, A.6    Rösch, P.7
  • 79
    • 0026325233 scopus 로고
    • Towards protein tertiary fold prediction using distance and motif constraints
    • Taylor W. R. Towards protein tertiary fold prediction using distance and motif constraints. Protein Eng. 4:1991;853-870.
    • (1991) Protein Eng. , vol.4 , pp. 853-870
    • Taylor, W.R.1
  • 80
    • 0027952860 scopus 로고
    • Compensating changes in protein multiple sequence alignments
    • Taylor W. R., Harrick K. Compensating changes in protein multiple sequence alignments. Protein Eng. 7:1994;342-348.
    • (1994) Protein Eng. , vol.7 , pp. 342-348
    • Taylor, W.R.1    Harrick, K.2
  • 81
    • 0025834829 scopus 로고
    • Analysis of protein main-chain solvation as a function of secondary structure
    • Thanki N., Umrania Y., Thornton J. M., Goodfellow J. M. Analysis of protein main-chain solvation as a function of secondary structure. J. Mol. Biol. 221:1991;669-691.
    • (1991) J. Mol. Biol. , vol.221 , pp. 669-691
    • Thanki, N.1    Umrania, Y.2    Thornton, J.M.3    Goodfellow, J.M.4
  • 82
    • 0029850738 scopus 로고    scopus 로고
    • The prediction of protein contacts from multiple sequence alignments
    • Thomas D., Casari G., Sander G. The prediction of protein contacts from multiple sequence alignments. Protein Eng. 9:1996;941-948.
    • (1996) Protein Eng. , vol.9 , pp. 941-948
    • Thomas, D.1    Casari, G.2    Sander, G.3
  • 83
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • Thompson J. D., Higgins D. G., Gibson T. J. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. Biosci. 10:1994;19-29.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 85
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modelling and drug design program
    • Vriend G. WHAT IF: a molecular modelling and drug design program. J. Mol. Graph. 8:1990;52-56.
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 88
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • V. Bryson, & H. J. Vogel. New York: Academic Press
    • Zuckerkandl E., Pauling L. Evolutionary divergence and convergence in proteins. Bryson V., Vogel H. J. Evolving Genes And Proteins. 1965;97-166 Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2
  • 89
    • 0023660653 scopus 로고
    • Prediction of protein secondary structure and active sites using alignment of homologous sequences
    • Zvelebil M. J., Barton G. J., Taylor W. R., Sternberg M. J. E. Prediction of protein secondary structure and active sites using alignment of homologous sequences. J. Mol. Biol. 195:1987;957-961.
    • (1987) J. Mol. Biol. , vol.195 , pp. 957-961
    • Zvelebil, M.J.1    Barton, G.J.2    Taylor, W.R.3    Sternberg, M.J.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.