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Volumn 6, Issue 8, 1997, Pages 1661-1681

Bayesian statistical analysis of protein side-chain rotamer preferences

Author keywords

Bayesian statistics; Molecular mechanics; Protein structure; Rotamers; Side chains

Indexed keywords

PROTEIN;

EID: 1842326139     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060807     Document Type: Article
Times cited : (693)

References (45)
  • 4
    • 0031576989 scopus 로고    scopus 로고
    • Homology modeling with a backbone-dependent rotamer library
    • Bower M, Cohen FE, Dunbrack RL Jr. 1997. Homology modeling with a backbone-dependent rotamer library. J Mol Biol 267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.1    Cohen, F.E.2    Dunbrack Jr., R.L.3
  • 5
    • 0028247281 scopus 로고
    • Side-chain entropy and packing in proteins
    • Bromberg S, Dill KA. 1994. Side-chain entropy and packing in proteins. Protein Sci 3:997-1009.
    • (1994) Protein Sci , vol.3 , pp. 997-1009
    • Bromberg, S.1    Dill, K.A.2
  • 7
    • 0014885326 scopus 로고
    • Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins
    • Chandrasekaran R, Ramachandran GN. 1970. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins. Int J Pept Prot Res 2:223-233.
    • (1970) Int J Pept Prot Res , vol.2 , pp. 223-233
    • Chandrasekaran, R.1    Ramachandran, G.N.2
  • 9
    • 0015691271 scopus 로고
    • Conformational analysis of aromatic amino acids by X-ray crystallography
    • Cody V, Duax WL, Hauptman H. 1973. Conformational analysis of aromatic amino acids by X-ray crystallography. Int J Pept Prot Res 5:297-308.
    • (1973) Int J Pept Prot Res , vol.5 , pp. 297-308
    • Cody, V.1    Duax, W.L.2    Hauptman, H.3
  • 10
    • 33847087644 scopus 로고
    • Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane
    • Compton DAC, Montera S, Murphy WF. 1980. Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane. J Phys Chem 84:3587-3591.
    • (1980) J Phys Chem , vol.84 , pp. 3587-3591
    • Compton, D.A.C.1    Montera, S.2    Murphy, W.F.3
  • 13
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack RL Jr, Karplus M. 1993. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J Mol Biol 230:543-571.
    • (1993) J Mol Biol , vol.230 , pp. 543-571
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 14
    • 0028429178 scopus 로고
    • Conformational analysis of the backbone-dependent rotamer preferences of protein side chains
    • Dunbrack RL Jr, Karplus M. 1994. Conformational analysis of the backbone-dependent rotamer preferences of protein side chains. Nature Struct Biol 1:334-340.
    • (1994) Nature Struct Biol , vol.1 , pp. 334-340
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 15
    • 0000049763 scopus 로고
    • 3v rotors. 12. Low frequency vibrational spectra, methyl torsional potential function, and internal rotation of n-butane
    • 3v rotors. 12. Low frequency vibrational spectra, methyl torsional potential function, and internal rotation of n-butane. J Phys Chem 83:265-268.
    • (1979) J Phys Chem , vol.83 , pp. 265-268
    • Durig, J.R.1    Compton, D.A.C.2
  • 16
    • 0018780591 scopus 로고
    • Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment
    • Gelin BR, Karplus M. 1979. Side-chain torsional potentials: Effect of dipeptide, protein, and solvent environment. Biochemistry 18:1256-1268.
    • (1979) Biochemistry , vol.18 , pp. 1256-1268
    • Gelin, B.R.1    Karplus, M.2
  • 18
    • 0027102226 scopus 로고
    • OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
    • Heringa J, Sommerfeldt H, Higgins D, Argos P. 1992. OBSTRUCT: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. CABIOS 8:599-600.
    • (1992) CABIOS , vol.8 , pp. 599-600
    • Heringa, J.1    Sommerfeldt, H.2    Higgins, D.3    Argos, P.4
  • 19
    • 0020685129 scopus 로고
    • Structure and refinement of penicillopepsin at 1.8 Å resolution
    • James MNG, Sielecki AR. 1983. Structure and refinement of penicillopepsin at 1.8 Å resolution. J Mol Biol 163:299-361.
    • (1983) J Mol Biol , vol.163 , pp. 299-361
    • James, M.N.G.1    Sielecki, A.R.2
  • 20
    • 0018115846 scopus 로고
    • Conformations of amino acid side chains in proteins
    • Janin J, Wodak S, Levitt M, Maigret B. 1978. Conformations of amino acid side chains in proteins. J Mol Biol 125:357-386.
    • (1978) J Mol Biol , vol.125 , pp. 357-386
    • Janin, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 21
    • 0000584319 scopus 로고
    • An approach to the internal rotation problem
    • Karplus M, Parr RG. 1963. An approach to the internal rotation problem. J Chem Phys 38:1547-1552.
    • (1963) J Chem Phys , vol.38 , pp. 1547-1552
    • Karplus, M.1    Parr, R.G.2
  • 22
    • 33947347962 scopus 로고
    • The entropy of ethane and the third law of thermodynamics. Hindered rotation of methyl groups
    • Kemp JD, Pitzer KS. 1937. The entropy of ethane and the third law of thermodynamics. Hindered rotation of methyl groups. J Am Chem Soc 59:276-279.
    • (1937) J Am Chem Soc , vol.59 , pp. 276-279
    • Kemp, J.D.1    Pitzer, K.S.2
  • 23
    • 0030000912 scopus 로고    scopus 로고
    • Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases
    • Kuszewski J, Gronenborn AM, Clore GM. 1996. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases. Protein Sci 5:1067-1080.
    • (1996) Protein Sci , vol.5 , pp. 1067-1080
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 24
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M. 1992. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226:507-533.
    • (1992) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 25
    • 84987317310 scopus 로고
    • Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl N′-methyl amides of the twenty naturally occurring amino acids
    • Lewis PN, Momany FA, Scheraga HA. 1973. Energy parameters in polypeptides. VI. Conformational energy analysis of the N-acetyl N′-methyl amides of the twenty naturally occurring amino acids. Israel J Chem 11:121-152.
    • (1973) Israel J Chem , vol.11 , pp. 121-152
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 26
    • 0030546797 scopus 로고    scopus 로고
    • Comparing theoretical and experimental backbone-dependent side-chain conformational preferences for linear, branched, aromatic, and polar residues
    • Marcus E, Keller DA, Shibata M, Ornstein RL, Rein R. 1996. Comparing theoretical and experimental backbone-dependent side-chain conformational preferences for linear, branched, aromatic, and polar residues. Chem Phys 204:157-171.
    • (1996) Chem Phys , vol.204 , pp. 157-171
    • Marcus, E.1    Keller, D.A.2    Shibata, M.3    Ornstein, R.L.4    Rein, R.5
  • 27
    • 1842390615 scopus 로고    scopus 로고
    • Seattle: Data Analysis Products Division, MathSoft
    • MathSoft. 1996. S-PLUS 3.4 for Unix. Seattle: Data Analysis Products Division, MathSoft.
    • (1996) S-PLUS 3.4 for Unix
  • 28
    • 0023521842 scopus 로고
    • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
    • McGregor MJ, Islam SA, Sternberg MJE. 1987. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J Mol Biol 198:295-310.
    • (1987) J Mol Biol , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.J.E.3
  • 29
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • Moult J, James MNG. 1986. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins Strict Funct Genet 1:146-163.
    • (1986) Proteins Strict Funct Genet , vol.1 , pp. 146-163
    • Moult, J.1    James, M.N.G.2
  • 30
    • 0028342488 scopus 로고
    • A statistical analysis of side-chain conformations in proteins - Comparison with ECEPP predictions
    • Nayeem A, Scheraga HA. 1994. A statistical analysis of side-chain conformations in proteins - Comparison with ECEPP predictions. J Protein Chem 13:283-296.
    • (1994) J Protein Chem , vol.13 , pp. 283-296
    • Nayeem, A.1    Scheraga, H.A.2
  • 31
    • 33947445123 scopus 로고
    • Chemical equilibria, free energies, and heat contents for gaseous hydrocarbons
    • Pitzer KS. 1940a. Chemical equilibria, free energies, and heat contents for gaseous hydrocarbons. Chem Rev 27:39-57.
    • (1940) Chem Rev , vol.27 , pp. 39-57
    • Pitzer, K.S.1
  • 32
    • 36849125469 scopus 로고
    • The vibration frequencies and thermodynamic functions of long chain hydrocarbons
    • Pitzer KS. 1940b. The vibration frequencies and thermodynamic functions of long chain hydrocarbons. J Chem Phys 8:711-720.
    • (1940) J Chem Phys , vol.8 , pp. 711-720
    • Pitzer, K.S.1
  • 33
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM. 1987. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193:775-792.
    • (1987) J Mol Biol , vol.193 , pp. 775-792
    • Ponder, J.W.1    Richards, F.M.2
  • 34
    • 0014979318 scopus 로고
    • Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit
    • Ponnuswamy PK, Sasisekharan V. 1971. Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit. Biopolymers 10:565-582.
    • (1971) Biopolymers , vol.10 , pp. 565-582
    • Ponnuswamy, P.K.1    Sasisekharan, V.2
  • 36
    • 0016022524 scopus 로고
    • Molecular orbital calculations on the conformation of amino acid residues of proteins
    • Pullman B, Pullman A. 1974. Molecular orbital calculations on the conformation of amino acid residues of proteins. Adv Protein Chem 28:347-526.
    • (1974) Adv Protein Chem , vol.28 , pp. 347-526
    • Pullman, B.1    Pullman, A.2
  • 37
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Šali A, Blundell TL. 1993. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Šali, A.1    Blundell, T.L.2
  • 38
    • 0014983538 scopus 로고
    • Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl, aromatic side groups in a dipeptide unit
    • Sasisekharan V, Ponnuswamy PK. 1971. Studies on the conformation of amino acids. X. Conformations of norvalyl, leucyl, aromatic side groups in a dipeptide unit. Biopolymers 10:583-592.
    • (1971) Biopolymers , vol.10 , pp. 583-592
    • Sasisekharan, V.1    Ponnuswamy, P.K.2
  • 39
    • 0027208112 scopus 로고
    • Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins
    • Schrauber H, Eisenhaber F, Argos P. 1993. Rotamers: To be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 230:592-612.
    • (1993) J Mol Biol , vol.230 , pp. 592-612
    • Schrauber, H.1    Eisenhaber, F.2    Argos, P.3
  • 40
    • 0024742246 scopus 로고
    • Theory of cooperative transitions in protein molecules 1. Why denaturation of globular protein is a first-order phase transition
    • Shakhnovich EI, Finkelstein AV. 1989. Theory of cooperative transitions in protein molecules 1. Why denaturation of globular protein is a first-order phase transition. Biopolymers 28:1667-1680.
    • (1989) Biopolymers , vol.28 , pp. 1667-1680
    • Shakhnovich, E.I.1    Finkelstein, A.V.2
  • 41
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based predictions of local structures in globular proteins
    • Sippl MJ. 1990. Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based predictions of local structures in globular proteins. J Mol Biol 213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 42
    • 0000179199 scopus 로고
    • Knowledge-based modeling of homologous proteins, Part II: Rules for the conformations of substituted side chains
    • Sutcliffe MJ, Hayes FR, Blundell TL. 1987. Knowledge-based modeling of homologous proteins, Part II: Rules for the conformations of substituted side chains. Protein Eng 1:385-392.
    • (1987) Protein Eng , vol.1 , pp. 385-392
    • Sutcliffe, M.J.1    Hayes, F.R.2    Blundell, T.L.3
  • 43
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side-chain conformations
    • Tuffery P, Etchebest C, Hazout S, Lavery R. 1991. A new approach to the rapid determination of protein side-chain conformations. J Biomol Str Dynam 8:1267-1289.
    • (1991) J Biomol Str Dynam , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 44
    • 33845279881 scopus 로고
    • Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions
    • Wiberg KB, Murcko MA. 1988. Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions. J Am Chem Soc 110:8029-8038.
    • (1988) J Am Chem Soc , vol.110 , pp. 8029-8038
    • Wiberg, K.B.1    Murcko, M.A.2
  • 45
    • 0017858839 scopus 로고
    • Influence of local interactions on protein structure. IV. Conformational energy studies of N-acetyl-N′-methylamides of Ser-X and X-Ser dipeptides
    • Zimmerman SS, Scheraga HA. 1978. Influence of local interactions on protein structure. IV. Conformational energy studies of N-acetyl-N′-methylamides of Ser-X and X-Ser dipeptides. Biopolymers 17:1885-1890.
    • (1978) Biopolymers , vol.17 , pp. 1885-1890
    • Zimmerman, S.S.1    Scheraga, H.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.