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Volumn 67, Issue 1, 2007, Pages 142-153

A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction

Author keywords

ab initio; Contact prediction; Correlated mutations

Indexed keywords

AMINO ACID; PROTEIN;

EID: 33847356936     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21223     Document Type: Article
Times cited : (31)

References (50)
  • 1
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003;85:1145-1164.
    • (2003) Biophys J , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 2
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • Schueler-Furman O, Wang C, Bradley P, Kira M, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
    • (2005) Science , vol.310 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Kira, M.4    Baker, D.5
  • 4
    • 30344475200 scopus 로고    scopus 로고
    • Progress over the first decade of CASP experiments
    • Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61 (Suppl 7):225-236.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 225-236
    • Kryshtafovych, A.1    Venclovas, C.2    Fidelis, K.3    Moult, J.4
  • 5
    • 0032477713 scopus 로고    scopus 로고
    • Nativelike topology assembly of small proteins using predicted restraints to monte carlo folding simulations
    • Ortiz A, Kolinski A, Skolnick J. Nativelike topology assembly of small proteins using predicted restraints to monte carlo folding simulations. Proc Natl Acad Sci USA 1998;95:1020-1025.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 1020-1025
    • Ortiz, A.1    Kolinski, A.2    Skolnick, J.3
  • 6
    • 0001691450 scopus 로고    scopus 로고
    • Protein fold determination from sparse distance restraints: The restrained generic direct Monte Carlo method
    • Debe D, Carlson M, Sadanobu J, Chan S, Goddard W. Protein fold determination from sparse distance restraints: the restrained generic direct Monte Carlo method. J Phys Chem B 1999;103:3001-3008.
    • (1999) J Phys Chem B , vol.103 , pp. 3001-3008
    • Debe, D.1    Carlson, M.2    Sadanobu, J.3    Chan, S.4    Goddard, W.5
  • 8
    • 0023660022 scopus 로고
    • Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh D, Lesk A, Bloomer A, Klug C. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 1987;193:693-707.
    • (1987) J Mol Biol , vol.193 , pp. 693-707
    • Altschuh, D.1    Lesk, A.2    Bloomer, A.3    Klug, C.4
  • 9
    • 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 1994;91:98-102.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 98-102
    • Neher, E.1
  • 10
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations
    • Shindyalov I, Kolchanov N, Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations. Protein Eng 1994;7:349-358.
    • (1994) Protein Eng , vol.7 , pp. 349-358
    • Shindyalov, I.1    Kolchanov, N.2    Sander, C.3
  • 11
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Gobel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 12
    • 0036721218 scopus 로고    scopus 로고
    • Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations
    • Kass I, Horovitz A Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 2002;48:611-617.
    • (2002) Proteins , vol.48 , pp. 611-617
    • Kass, I.1    Horovitz, A.2
  • 13
    • 0033550256 scopus 로고    scopus 로고
    • Effective use of sequence correlation and conservation in fold recognition
    • Olemea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
    • (1999) J Mol Biol , vol.293 , pp. 1221-1239
    • Olemea, O.1    Rost, B.2    Valencia, A.3
  • 14
    • 0036568319 scopus 로고    scopus 로고
    • In silico two-hybrid system for the selection of physically interacting protein pairs
    • Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 2002;47:219-227.
    • (2002) Proteins , vol.47 , pp. 219-227
    • Pazos, F.1    Valencia, A.2
  • 16
    • 0029164276 scopus 로고
    • Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis
    • Singer M, Oliveira L, Vriend G, Shepherd G. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis. Receptors Channels 1995;3:89-95.
    • (1995) Receptors Channels , vol.3 , pp. 89-95
    • Singer, M.1    Oliveira, L.2    Vriend, G.3    Shepherd, G.4
  • 17
    • 0015243774 scopus 로고
    • Tests for comparing related amino acid sequences
    • McLachlan A. Tests for comparing related amino acid sequences. J Mol Biol 1971;61:409-424.
    • (1971) J Mol Biol , vol.61 , pp. 409-424
    • McLachlan, A.1
  • 18
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff J. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.2
  • 19
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using patterns of correlation
    • Hamilton N, Burrage K, Ragan M, Huber T. Protein contact prediction using patterns of correlation. Proteins 2004;56:679-684.
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.3    Huber, T.4
  • 20
    • 1842464687 scopus 로고    scopus 로고
    • Inter-residue interactions in protein folding and stability
    • Gromiha MM, Selvaraj S. Inter-residue interactions in protein folding and stability. Prog Biophys Mol Biol 2004;86:235-277.
    • (2004) Prog Biophys Mol Biol , vol.86 , pp. 235-277
    • Gromiha, M.M.1    Selvaraj, S.2
  • 21
    • 20844452182 scopus 로고    scopus 로고
    • Detection and reduction of evolutionary noise in correlated mutation analysis
    • Noivirt O, Eisenstein M, Horovitz A. Detection and reduction of evolutionary noise in correlated mutation analysis. Protein Eng 2005;18:247-253.
    • (2005) Protein Eng , vol.18 , pp. 247-253
    • Noivirt, O.1    Eisenstein, M.2    Horovitz, A.3
  • 23
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: A general method for a comparative analysis of discrete characters
    • Pagel M. Detecting correlated evolution on phylogenies: a general method for a comparative analysis of discrete characters. Proc R Soc Lond 1994;255:37-45.
    • (1994) Proc R Soc Lond , vol.255 , pp. 37-45
    • Pagel, M.1
  • 24
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • Pollock D, Taylor W. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng 1997;10:647-657.
    • (1997) Protein Eng , vol.10 , pp. 647-657
    • Pollock, D.1    Taylor, W.2
  • 25
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock D, Taylor W, Goldman N. Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol 1999;287:187-198.
    • (1999) J Mol Biol , vol.287 , pp. 187-198
    • Pollock, D.1    Taylor, W.2    Goldman, N.3
  • 26
    • 0033744204 scopus 로고    scopus 로고
    • Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
    • Tuffery P, Darlu P. Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol Biol Evol 2000;17:1753-1759.
    • (2000) Mol Biol Evol , vol.17 , pp. 1753-1759
    • Tuffery, P.1    Darlu, P.2
  • 27
    • 2942580743 scopus 로고    scopus 로고
    • An evolutionary conserved network of amino acids mediates gating in voltage dependent potassium channels
    • Fleishman S, Yifrach O, Ben-Tal N. An evolutionary conserved network of amino acids mediates gating in voltage dependent potassium channels. J Mol Biol 2004;340:307-318.
    • (2004) J Mol Biol , vol.340 , pp. 307-318
    • Fleishman, S.1    Yifrach, O.2    Ben-Tal, N.3
  • 28
    • 0242299187 scopus 로고    scopus 로고
    • Predictions without templates: New folds, secondary structure, and contacts in CASP5
    • Aloy P, Stark A, Hadley C, Russell R. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins 2003;53 (Suppl 6):436-456.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 436-456
    • Aloy, P.1    Stark, A.2    Hadley, C.3    Russell, R.4
  • 29
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001;14:835-843.
    • (2001) Protein Eng , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 30
    • 0029850738 scopus 로고    scopus 로고
    • The prediction of protein contacts from multiple sequence alignments
    • Thomas DJ, Casari G, Sander C. The prediction of protein contacts from multiple sequence alignments. Protein Eng 1996;9:941-948.
    • (1996) Protein Eng , vol.9 , pp. 941-948
    • Thomas, D.J.1    Casari, G.2    Sander, C.3
  • 31
    • 0036763251 scopus 로고    scopus 로고
    • Prediction of protein residue contacts with a PDB-derived likelihood matrix
    • Singer M, Vriend G, Bywater R. Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Eng 2002;15:721-725.
    • (2002) Protein Eng , vol.15 , pp. 721-725
    • Singer, M.1    Vriend, G.2    Bywater, R.3
  • 32
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff S, Henikoff J. Position-based sequence weights. J Mol Biol 1994;243:574-578.
    • (1994) J Mol Biol , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.2
  • 33
    • 0026410103 scopus 로고
    • Automated assembly of protein blocks for database searching
    • Henikoff J, Henikoff S. Automated assembly of protein blocks for database searching. Nucleic Acids Res 1991;19:6565-6572.
    • (1991) Nucleic Acids Res , vol.19 , pp. 6565-6572
    • Henikoff, J.1    Henikoff, S.2
  • 34
    • 0032776495 scopus 로고    scopus 로고
    • Blocks+: A nonredundant database of protein alignment blocks derived from multiple compilations
    • Henikoff S, Henikoff J, Pietrokovski S. Blocks+: a nonredundant database of protein alignment blocks derived from multiple compilations. Bioinformatics 1999;15:471-479.
    • (1999) Bioinformatics , vol.15 , pp. 471-479
    • Henikoff, S.1    Henikoff, J.2    Pietrokovski, S.3
  • 37
    • 0036773411 scopus 로고    scopus 로고
    • Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
    • McConkey B, Sobolev V, Edelman M. Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure. Bioinformatics 2002;18:1365-1373.
    • (2002) Bioinformatics , vol.18 , pp. 1365-1373
    • McConkey, B.1    Sobolev, V.2    Edelman, M.3
  • 38
    • 0034308172 scopus 로고    scopus 로고
    • Discriminating between homodimeric and monomeric proteins in the crystalline state
    • Ponstingl H, Henrick K, Thornton J. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000;41:47-57.
    • (2000) Proteins , vol.41 , pp. 47-57
    • Ponstingl, H.1    Henrick, K.2    Thornton, J.3
  • 40
    • 0030927252 scopus 로고    scopus 로고
    • A graphical interface for correlated mutations and other protein structure prediction methods
    • Pazos F, Olmea O, Valencia A. A graphical interface for correlated mutations and other protein structure prediction methods. Comput Appl Biosci 1997;13:319-321.
    • (1997) Comput Appl Biosci , vol.13 , pp. 319-321
    • Pazos, F.1    Olmea, O.2    Valencia, A.3
  • 41
    • 0030627941 scopus 로고    scopus 로고
    • Improving contact predictions by the combination of correlated mutations and sources of sequence information
    • Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and sources of sequence information. Fold Des 1997;2:S25-S32.
    • (1997) Fold Des , vol.2
    • Olmea, O.1    Valencia, A.2
  • 42
    • 0031841279 scopus 로고    scopus 로고
    • The HSSP database of protein structure-sequence alignments and family profiles
    • Dodge C, Schneider R, Sander C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res 1998;26:313-315.
    • (1998) Nucleic Acids Res , vol.26 , pp. 313-315
    • Dodge, C.1    Schneider, R.2    Sander, C.3
  • 43
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks-based regression
    • Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 2004;56:753-767.
    • (2004) Proteins , vol.56 , pp. 753-767
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 44
    • 2442665257 scopus 로고    scopus 로고
    • Protein decoy sets for evaluating energy functions
    • Gilis D. Protein decoy sets for evaluating energy functions. J Biomol Struct Dyn 2004;21:725-736.
    • (2004) J Biomol Struct Dyn , vol.21 , pp. 725-736
    • Gilis, D.1
  • 45
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai J, Bonneau R, Morozov A, Kuhlman B, Rohl C, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003;53:76-87.
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.3    Kuhlman, B.4    Rohl, C.5    Baker, D.6
  • 46
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000;9:1399-1401.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 47
    • 0028895567 scopus 로고
    • Discriminating compact nonnative structures from the native structure of globular proteins
    • Wang Y, Zhang H, Li W, Scott R. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 709-713
    • Wang, Y.1    Zhang, H.2    Li, W.3    Scott, R.4
  • 48
    • 3042842115 scopus 로고    scopus 로고
    • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments
    • Fodor A, Aldrich R. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 2004;56:211-221.
    • (2004) Proteins , vol.56 , pp. 211-221
    • Fodor, A.1    Aldrich, R.2
  • 49
    • 13944252115 scopus 로고    scopus 로고
    • Prediction of distant residue contacts with the use of evolutionary information
    • Vicatos S, Reddy B, Kaznessis Y. Prediction of distant residue contacts with the use of evolutionary information. Proteins 2005;58:935-949.
    • (2005) Proteins , vol.58 , pp. 935-949
    • Vicatos, S.1    Reddy, B.2    Kaznessis, Y.3
  • 50
    • 0035700864 scopus 로고    scopus 로고
    • Progress in predicting inter-residue contacts of proteins with neural network and correlated mutations
    • Fariselli P, Olemea O, Valencia A, Casadio R. Progress in predicting inter-residue contacts of proteins with neural network and correlated mutations. Proteins 2001;45 (Suppl 5):157-162.
    • (2001) Proteins , vol.45 , Issue.SUPPL. 5 , pp. 157-162
    • Fariselli, P.1    Olemea, O.2    Valencia, A.3    Casadio, R.4


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