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Volumn 15, Issue 2, 2008, Pages 165-184

Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules

Author keywords

Algorithms; Computational molecular biology; Electrostatics; pK; Statistical mechanics

Indexed keywords

AMINO ACID;

EID: 40049098280     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.0144     Document Type: Article
Times cited : (39)

References (43)
  • 1
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J., McCammon, J.A., and Gilson, M.K. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436.
    • (1994) J. Mol. Biol , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 2
    • 0038813543 scopus 로고    scopus 로고
    • One-dimensional Ising model applied to protein folding
    • Bakk, A., and Høye, J.S. 2003. One-dimensional Ising model applied to protein folding. Phys. A Stat. Mech. App. 323, 504-518.
    • (2003) Phys. A Stat. Mech. App , vol.323 , pp. 504-518
    • Bakk, A.1    Høye, J.S.2
  • 3
    • 0001051761 scopus 로고
    • On the computational complexity of Ising spin glass models
    • Barahona, F. 1982. On the computational complexity of Ising spin glass models. J. Phys. A Math. Gen. 15, 3241-3253.
    • (1982) J. Phys. A Math. Gen , vol.15 , pp. 3241-3253
    • Barahona, F.1
  • 4
    • 0025197061 scopus 로고
    • pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • Bashford, D., and Karplus, M. 1990. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29, 10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 5
    • 33751499830 scopus 로고
    • Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation
    • Bashford, D., and Karplus, M. 1991. Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation. J. Phys. Chem. 95, 9556-9561.
    • (1991) J. Phys. Chem , vol.95 , pp. 9556-9561
    • Bashford, D.1    Karplus, M.2
  • 7
    • 0026095641 scopus 로고
    • Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of rhodobacter sphaeroides
    • Beroza, P., Fredkin, D.R., Okamura, M.Y., et al. 1991. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 88, 5804-5808.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 5804-5808
    • Beroza, P.1    Fredkin, D.R.2    Okamura, M.Y.3
  • 8
    • 0034676459 scopus 로고    scopus 로고
    • Mean-field cluster model for the critical behavior of ferromagnets
    • Chamberlin, R.V. 2000. Mean-field cluster model for the critical behavior of ferromagnets. Nature 408, 337-339.
    • (2000) Nature , vol.408 , pp. 337-339
    • Chamberlin, R.V.1
  • 9
    • 68249119557 scopus 로고    scopus 로고
    • The Ising model is NP-complete
    • Cipra, B.A. 2000. The Ising model is NP-complete. SIAM News 33(6), 1-3.
    • (2000) SIAM News , vol.33 , Issue.6 , pp. 1-3
    • Cipra, B.A.1
  • 12
    • 33748593093 scopus 로고    scopus 로고
    • as of ionizable groups in proteins
    • as of ionizable groups in proteins. J. Phys. Chem. 100, 17373-17387.
    • (1996) J. Phys. Chem , vol.100 , pp. 17373-17387
    • Demchuk, E.1    Wade, R.C.2
  • 13
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein side-chain positioning
    • Desmet, J., de Maeyer, M., Hazes, B., and Lasters, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539-542.
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    de Maeyer, M.2    Hazes, B.3    Lasters, I.4
  • 14
    • 40049105362 scopus 로고    scopus 로고
    • Garliauskas, A. 2006. Nonlinearities in artificial neural systems interpreted as an application of Ising physics. Nonlinear Anal. Modelling Control 11, 367-383.
    • Garliauskas, A. 2006. Nonlinearities in artificial neural systems interpreted as an application of Ising physics. Nonlinear Anal. Modelling Control 11, 367-383.
  • 16
    • 0027477251 scopus 로고
    • Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins
    • Gilson, M.K. 1993. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15, 266-282.
    • (1993) Proteins , vol.15 , pp. 266-282
    • Gilson, M.K.1
  • 17
    • 0023899747 scopus 로고
    • Energetics of charge-charge interactions in proteins
    • Gilson, M.K., and Honig, B.H. 1988. Energetics of charge-charge interactions in proteins. Proteins 3, 32-52.
    • (1988) Proteins , vol.3 , pp. 32-52
    • Gilson, M.K.1    Honig, B.H.2
  • 19
  • 20
    • 23144457576 scopus 로고    scopus 로고
    • HCC: A server for estimating pKa's and adding missing hydrogens to macromolecules
    • Gordon, J.C., Myers, J.B., Folta, T., et al. 2005. HCC: a server for estimating pKa's and adding missing hydrogens to macromolecules. Nucl. Acids Res. 33, 368-371.
    • (2005) Nucl. Acids Res , vol.33 , pp. 368-371
    • Gordon, J.C.1    Myers, J.B.2    Folta, T.3
  • 21
    • 0037107898 scopus 로고    scopus 로고
    • Calculation of partition function using quantum genetic algorithms
    • Grigorenko, I., and Garcia, M.E. 2002. Calculation of partition function using quantum genetic algorithms. Phys. A Stat. Mech. App. 313, 463-470.
    • (2002) Phys. A Stat. Mech. App , vol.313 , pp. 463-470
    • Grigorenko, I.1    Garcia, M.E.2
  • 24
    • 0033727269 scopus 로고    scopus 로고
    • Statistical mechanics, three-dimensionality and NP-completeness: I. Universality of intractability of the partition functions of the Ising model across non-planar lattices
    • Istrail, S. 2001. Statistical mechanics, three-dimensionality and NP-completeness: I. Universality of intractability of the partition functions of the Ising model across non-planar lattices. Proc. 32nd ACM Symp. Theory Comput. 87-96.
    • (2001) Proc. 32nd ACM Symp. Theory Comput , pp. 87-96
    • Istrail, S.1
  • 26
    • 0027677367 scopus 로고
    • Polynomial-time approximation algorithms for the Ising model
    • Jerrum, M., and Sinclair, A. 1993. Polynomial-time approximation algorithms for the Ising model. SIAM J. Comput. 22, 1087-1116.
    • (1993) SIAM J. Comput , vol.22 , pp. 1087-1116
    • Jerrum, M.1    Sinclair, A.2
  • 29
    • 0031058410 scopus 로고    scopus 로고
    • NMR structure of the 35-residue villin headpiece subdomain
    • McKnight, C.J., Matsudaira, P.T., and Kim, P.S. 1997. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4, 180-184.
    • (1997) Nat. Struct. Biol , vol.4 , pp. 180-184
    • McKnight, C.J.1    Matsudaira, P.T.2    Kim, P.S.3
  • 30
    • 33646794930 scopus 로고    scopus 로고
    • A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
    • Myers, J., Grothaus, G., Narayanan, S., et al. 2006. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins 63, 928-938.
    • (2006) Proteins , vol.63 , pp. 928-938
    • Myers, J.1    Grothaus, G.2    Narayanan, S.3
  • 31
    • 22044449827 scopus 로고    scopus 로고
    • The signature of the internal partition function in thermodynamical quantities of the solar interior
    • Nayfonov, A., and Däppen, W. 1998. The signature of the internal partition function in thermodynamical quantities of the solar interior. Astrophys. J. 499, 489-495.
    • (1998) Astrophys. J , vol.499 , pp. 489-495
    • Nayfonov, A.1    Däppen, W.2
  • 32
    • 0042011188 scopus 로고    scopus 로고
    • a values in enzyme active sites
    • a values in enzyme active sites. Prot. Sci. 12, 1894-1901.
    • (2003) Prot. Sci , vol.12 , pp. 1894-1901
    • Nielsen, J.1    McCammon, J.2
  • 34
    • 0042386423 scopus 로고    scopus 로고
    • Proton affinity changes during unidirectional proton transport in the bacteriorhodopsin photocycle
    • Onufriev, A., Smondyrev, A., and Bashford, D. 2003. Proton affinity changes during unidirectional proton transport in the bacteriorhodopsin photocycle. J. Mol. Biol. 332, 1183-1193.
    • (2003) J. Mol. Biol , vol.332 , pp. 1183-1193
    • Onufriev, A.1    Smondyrev, A.2    Bashford, D.3
  • 35
    • 0018094892 scopus 로고
    • Electrostatic effects in proteins
    • Perutz, M. 1978. Electrostatic effects in proteins. Science 201, 1187-1191.
    • (1978) Science , vol.201 , pp. 1187-1191
    • Perutz, M.1
  • 37
    • 0031719963 scopus 로고    scopus 로고
    • Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center
    • Rabenstein, B., Ullmann, G.M., and Knapp, E.W. 1998. Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center. Eur. Biophys. J. 27, 626-637.
    • (1998) Eur. Biophys. J , vol.27 , pp. 626-637
    • Rabenstein, B.1    Ullmann, G.M.2    Knapp, E.W.3
  • 40
    • 0000174762 scopus 로고    scopus 로고
    • Multiple-site ligand binding to flexible macromolecules. Separation of global and local conformational change and on iterative mobile clustering approach
    • Spassov, V.Z., and Bashford, D. 1999. Multiple-site ligand binding to flexible macromolecules. Separation of global and local conformational change and on iterative mobile clustering approach. J. Comp. Chem. 20, 1091-1111.
    • (1999) J. Comp. Chem , vol.20 , pp. 1091-1111
    • Spassov, V.Z.1    Bashford, D.2
  • 41
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • Tanford, C., and Kirkwood, J.G. 1957. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79, 5333-5339.
    • (1957) J. Am. Chem. Soc , vol.79 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 42
    • 0030612614 scopus 로고    scopus 로고
    • a changes in a protein tyrosine phosphatase: Experimental and theoretical determination of electrostatic properties in a small protein
    • a changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein. Biochemistry 36, 11984-11994.
    • (1997) Biochemistry , vol.36 , pp. 11984-11994
    • Tishmack, P.A.1    Bashford, D.2    Harms, E.3
  • 43
    • 0021480222 scopus 로고
    • Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability
    • Warshel, A., Russell, S.T., and Churg, A.K. 1984. Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability. Proc. Natl. Acad. Sci. USA 81, 4785-4789.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 4785-4789
    • Warshel, A.1    Russell, S.T.2    Churg, A.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.