메뉴 건너뛰기




Volumn 61, Issue 3, 2005, Pages 523-534

Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization

Author keywords

Amino acid physical properties; Amino acid similarity; Principal components analysis

Indexed keywords

GLYCINE;

EID: 27544433454     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20648     Document Type: Article
Times cited : (12)

References (47)
  • 1
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5: 113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 2
    • 0037433034 scopus 로고    scopus 로고
    • PCMA: Fast and accurate multiple sequence alignment based on profile consistency
    • Pei J, Sadreyev R, Grishin NV. PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 2003;19:427-428.
    • (2003) Bioinformatics , vol.19 , pp. 427-428
    • Pei, J.1    Sadreyev, R.2    Grishin, N.V.3
  • 3
    • 0242362175 scopus 로고    scopus 로고
    • Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance
    • Venclovas C. Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance. Proteins 2003;53(Suppl 6):380-388.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 380-388
    • Venclovas, C.1
  • 4
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci 2002;11:1702-1713.
    • (2002) Protein Sci , vol.11 , pp. 1702-1713
    • Jaroszewski, L.1    Li, W.2    Godzik, A.3
  • 6
    • 1842853736 scopus 로고    scopus 로고
    • Getting the most from your protein sequence
    • Copley RR, Russell RB. Getting the most from your protein sequence. Methods Mol Biol 2003;211:411-430.
    • (2003) Methods Mol Biol , vol.211 , pp. 411-430
    • Copley, R.R.1    Russell, R.B.2
  • 7
    • 0022591495 scopus 로고
    • The classification of amino acid conservation
    • Taylor WR. The classification of amino acid conservation. J Theor Biol 1986;119:205-218.
    • (1986) J Theor Biol , vol.119 , pp. 205-218
    • Taylor, W.R.1
  • 8
    • 0020528412 scopus 로고
    • What is a conservative substitution?
    • French S, Robson B. What is a conservative substitution? J Mol Evol 1983;19:171-175.
    • (1983) J Mol Evol , vol.19 , pp. 171-175
    • French, S.1    Robson, B.2
  • 10
    • 0030597348 scopus 로고    scopus 로고
    • A new approach to clustering the amino acids
    • Stanfel LE. A new approach to clustering the amino acids. J Theor Biol 1996;183:195-205.
    • (1996) J Theor Biol , vol.183 , pp. 195-205
    • Stanfel, L.E.1
  • 11
    • 0035789124 scopus 로고    scopus 로고
    • New quanitiative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties
    • Venkatarajan VS, Braun W. New quanitiative descriptors of amino acids based on multidimensional scaling of a large number of physical-chemical properties. J Mol Model 2001;7:445-453.
    • (2001) J Mol Model , vol.7 , pp. 445-453
    • Venkatarajan, V.S.1    Braun, W.2
  • 12
    • 1842477257 scopus 로고    scopus 로고
    • A new criterion and method for amino acid classification
    • Kosiol C, Goldman N, Buttimore NH. A new criterion and method for amino acid classification. J Theor Biol 2004;228:97-106.
    • (2004) J Theor Biol , vol.228 , pp. 97-106
    • Kosiol, C.1    Goldman, N.2    Buttimore, N.H.3
  • 13
    • 0038451355 scopus 로고    scopus 로고
    • Reduction of protein sequence complexity by residue grouping
    • Li T, Fan K, Wang J, Wang W. Reduction of protein sequence complexity by residue grouping. Protein Eng 2003;16:323-330.
    • (2003) Protein Eng , vol.16 , pp. 323-330
    • Li, T.1    Fan, K.2    Wang, J.3    Wang, W.4
  • 14
    • 0036677673 scopus 로고    scopus 로고
    • Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
    • Cannata N, Toppo S, Romualdi C, Valle G. Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices. Bioinformatics 2002;18:1102-1108.
    • (2002) Bioinformatics , vol.18 , pp. 1102-1108
    • Cannata, N.1    Toppo, S.2    Romualdi, C.3    Valle, G.4
  • 15
    • 0001338954 scopus 로고    scopus 로고
    • Simplified amino acid alphabets for protein fold recognition and implications for folding
    • Murphy LR, Wallqvist A, Levy RM. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng 2000;13:149-152.
    • (2000) Protein Eng , vol.13 , pp. 149-152
    • Murphy, L.R.1    Wallqvist, A.2    Levy, R.M.3
  • 16
    • 2542564988 scopus 로고    scopus 로고
    • A general clustering approach with application to the Miyazawa-Jernigan potentials for amino acids
    • Esteve JG, Falceto F. A general clustering approach with application to the Miyazawa-Jernigan potentials for amino acids. Proteins 2004;55:999-1004.
    • (2004) Proteins , vol.55 , pp. 999-1004
    • Esteve, J.G.1    Falceto, F.2
  • 18
    • 0032726679 scopus 로고    scopus 로고
    • A computational approach to simplifying the protein folding alphabet
    • Wang J, Wang W. A computational approach to simplifying the protein folding alphabet. Nat Struct Biol 1999;6:1033-1038.
    • (1999) Nat Struct Biol , vol.6 , pp. 1033-1038
    • Wang, J.1    Wang, W.2
  • 19
    • 0036836550 scopus 로고    scopus 로고
    • Discriminative ability with respect to amino acid types: Assessing the performance of knowledge-based potentials without threading
    • Kuznetsov IB, Rackovsky S. Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading. Proteins 2002;49:266-284.
    • (2002) Proteins , vol.49 , pp. 266-284
    • Kuznetsov, I.B.1    Rackovsky, S.2
  • 20
    • 0037103028 scopus 로고    scopus 로고
    • Optimally informative backbone structural propensities in proteins
    • Solis AD, Rackovsky S. Optimally informative backbone structural propensities in proteins. Proteins 2002;48:463-486.
    • (2002) Proteins , vol.48 , pp. 463-486
    • Solis, A.D.1    Rackovsky, S.2
  • 21
    • 0030332666 scopus 로고    scopus 로고
    • Discovering empirically conserved amino acid substitution groups in databases of protein families
    • Wu TD, Brutlag DL. Discovering empirically conserved amino acid substitution groups in databases of protein families. Proc Int Conf Intell Syst Mol Biol 1996;4:230-240.
    • (1996) Proc Int Conf Intell Syst Mol Biol , vol.4 , pp. 230-240
    • Wu, T.D.1    Brutlag, D.L.2
  • 22
    • 0031894593 scopus 로고    scopus 로고
    • Which effective property of amino acids is best preserved by the genetic code?
    • Trinquier G, Sanejouand YH. Which effective property of amino acids is best preserved by the genetic code? Protein Eng 1998;11: 153-169.
    • (1998) Protein Eng , vol.11 , pp. 153-169
    • Trinquier, G.1    Sanejouand, Y.H.2
  • 23
    • 0028081516 scopus 로고
    • Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
    • Tolstrup N, Toftgard J, Engelbrecht J, Brunak S. Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies. J Mol Biol 1994;243:816-820.
    • (1994) J Mol Biol , vol.243 , pp. 816-820
    • Tolstrup, N.1    Toftgard, J.2    Engelbrecht, J.3    Brunak, S.4
  • 24
    • 0018582090 scopus 로고
    • Water, protein folding, and the genetic code
    • Wolfenden RV, Cullis PM, Southgate CC. Water, protein folding, and the genetic code. Science 1979;206:575-577.
    • (1979) Science , vol.206 , pp. 575-577
    • Wolfenden, R.V.1    Cullis, P.M.2    Southgate, C.C.3
  • 26
    • 0022385890 scopus 로고
    • A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids
    • Sjostrom M, Wold S. A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids. J Mol Evol 1985;22:272-277.
    • (1985) J Mol Evol , vol.22 , pp. 272-277
    • Sjostrom, M.1    Wold, S.2
  • 27
    • 3042577367 scopus 로고    scopus 로고
    • De novo proteins from designed combinatorial libraries
    • Hecht MH, Das A, Go A, Bradley LH, Wei Y. De novo proteins from designed combinatorial libraries. Protein Sci 2004;13:1711-1723.
    • (2004) Protein Sci , vol.13 , pp. 1711-1723
    • Hecht, M.H.1    Das, A.2    Go, A.3    Bradley, L.H.4    Wei, Y.5
  • 29
    • 0021931978 scopus 로고
    • Statistical analysis of the physical properties of the 20 naturally occurring amino acids
    • Kidera A, Konishi Y, Oka M, Ooi T, Scheraga HA. Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J Protein Chem 1985;4:23-55.
    • (1985) J Protein Chem , vol.4 , pp. 23-55
    • Kidera, A.1    Konishi, Y.2    Oka, M.3    Ooi, T.4    Scheraga, H.A.5
  • 30
    • 8844234932 scopus 로고    scopus 로고
    • Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
    • Kinjo AR, Nishikawa K. Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins. Bioinformatics 2004;20:2504-2508.
    • (2004) Bioinformatics , vol.20 , pp. 2504-2508
    • Kinjo, A.R.1    Nishikawa, K.2
  • 31
    • 0346688667 scopus 로고    scopus 로고
    • An optimal structure-discriminative amino acid index for protein fold recognition
    • Leary RH, Rosen JB, Jambeck P. An optimal structure-discriminative amino acid index for protein fold recognition. Biophys J 2004;86:411-419.
    • (2004) Biophys J , vol.86 , pp. 411-419
    • Leary, R.H.1    Rosen, J.B.2    Jambeck, P.3
  • 32
    • 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. Nat Struct Biol 1995;2:171-178.
    • (1995) Nat Struct Biol , vol.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 33
    • 0026547387 scopus 로고
    • Sequence ordinations: A multivariate analysis approach to analysing large sequence data sets
    • Higgins DG. Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. Comput Appl Biosci 1992;8:15-22.
    • (1992) Comput Appl Biosci , vol.8 , pp. 15-22
    • Higgins, D.G.1
  • 34
    • 0032776495 scopus 로고    scopus 로고
    • Blocks+: A non-redundant database of protein alignment blocks derived from multiple compilations
    • Henikoff S, Henikoff JG, Pietrokovski S. Blocks+: a non-redundant 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.G.2    Pietrokovski, S.3
  • 37
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei J, Grishin NV. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 2001;17:700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 42
    • 0023055775 scopus 로고
    • New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: Correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites
    • Parker JM, Guo D, Hodges RS. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 1986;25:5425-5432.
    • (1986) Biochemistry , vol.25 , pp. 5425-5432
    • Parker, J.M.1    Guo, D.2    Hodges, R.S.3
  • 43
    • 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. Nucleic Acids Res 1996;24:206-209.
    • (1996) Nucleic Acids Res , vol.24 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 44
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 45
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 2003;326:317-336.
    • (2003) J Mol Biol , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 46
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A 1992;89:10915-10919.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 47
    • 0023232669 scopus 로고
    • Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues
    • Wold S, Eriksson L, Hellberg S, Jonsson J, Sjostrom M, Skagerberg B, Wikstrom C. Principal property values for six non-natural amino acids and their application to a structure-activity relationship for oxytocin peptide analogues. Can J Chem 1987;65:1814-1820.
    • (1987) Can J Chem , vol.65 , pp. 1814-1820
    • Wold, S.1    Eriksson, L.2    Hellberg, S.3    Jonsson, J.4    Sjostrom, M.5    Skagerberg, B.6    Wikstrom, C.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.