메뉴 건너뛰기




Volumn 19, Issue 1, 2014, Pages 45-50

Fragment-based error estimation in biomolecular modeling

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84891846172     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2013.08.016     Document Type: Review
Times cited : (5)

References (26)
  • 1
    • 0014675222 scopus 로고
    • Refinement of protein conformations using a macromolecular energy minimization procedure
    • M. Levitt, and S. Lifson Refinement of protein conformations using a macromolecular energy minimization procedure J. Mol. Biol. 46 1969 269 279
    • (1969) J. Mol. Biol. , vol.46 , pp. 269-279
    • Levitt, M.1    Lifson, S.2
  • 2
    • 34247133438 scopus 로고    scopus 로고
    • Error bars in experimental biology
    • G. Cumming et al. Error bars in experimental biology J. Cell Biol. 177 2007 7 11
    • (2007) J. Cell Biol. , vol.177 , pp. 7-11
    • Cumming, G.1
  • 3
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work for virtual library screening? An idealized computer experiment
    • R. Wang, and S. Wang How does consensus scoring work for virtual library screening? An idealized computer experiment J. Chem. Inform. Comput. Sci. 41 2001 1422 1426
    • (2001) J. Chem. Inform. Comput. Sci. , vol.41 , pp. 1422-1426
    • Wang, R.1    Wang, S.2
  • 4
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. 1. Nonpolar gases
    • R.W. Zwanzig High-temperature equation of state by a perturbation method. 1. Nonpolar gases J. Chem. Phys. 22 1954 1420 1426
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 5
    • 7044239742 scopus 로고
    • Free-energy calculations - Applications to chemical and biochemical phenomena
    • P. Kollman Free-energy calculations - applications to chemical and biochemical phenomena Chem. Rev. 93 1993 2395 2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 6
    • 84880011173 scopus 로고    scopus 로고
    • Calculating the sensitivity and robustness of binding free energy calculations to force field parameters
    • G.J. Rocklin et al. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters J. Chem. Theory Comput. 9 2013 3072 3083
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3072-3083
    • Rocklin, G.J.1
  • 7
    • 77952387014 scopus 로고    scopus 로고
    • Limits of free energy computation for protein-ligand interactions
    • K.M. Merz Limits of free energy computation for protein-ligand interactions J. Chem. Theory Comput. 6 2010 1769 1776
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1769-1776
    • Merz, K.M.1
  • 8
    • 79952090060 scopus 로고    scopus 로고
    • Formal estimation of errors in computed absolute interaction energies of protein-ligand complexes
    • J.C. Faver et al. Formal estimation of errors in computed absolute interaction energies of protein-ligand complexes J. Chem. Theory Comput. 7 2011 790 797
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 790-797
    • Faver, J.C.1
  • 9
    • 79955552707 scopus 로고    scopus 로고
    • The energy computation paradox and ab initio protein folding
    • J.C. Faver et al. The energy computation paradox and ab initio protein folding Plos One 6 2011 e18868
    • (2011) Plos One , vol.6 , pp. 18868
    • Faver, J.C.1
  • 10
    • 84867393067 scopus 로고    scopus 로고
    • The effects of computational modeling errors on the estimation of statistical mechanical variables
    • J.C. Faver et al. The effects of computational modeling errors on the estimation of statistical mechanical variables J. Chem. Theory Comput. 8 2012 3769 3776
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3769-3776
    • Faver, J.C.1
  • 11
    • 77953631827 scopus 로고    scopus 로고
    • A medicinal chemist's guide to molecular interactions
    • C. Bissantz et al. A medicinal chemist's guide to molecular interactions J. Med. Chem. 53 2010 5061 5084
    • (2010) J. Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1
  • 12
    • 0015859467 scopus 로고
    • Principles that govern folding of protein chains
    • C.B. Anfinsen Principles that govern folding of protein chains Science 181 1973 223 230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 13
    • 48249134448 scopus 로고    scopus 로고
    • The protein folding problem
    • K.A. Dill et al. The protein folding problem Ann. Rev. Biophys. 37 2008 289 316
    • (2008) Ann. Rev. Biophys. , vol.37 , pp. 289-316
    • Dill, K.A.1
  • 14
    • 0031022887 scopus 로고    scopus 로고
    • Additivity principles in biochemistry
    • K.A. Dill Additivity principles in biochemistry J. Biol. Chem. 272 1997 701 704
    • (1997) J. Biol. Chem. , vol.272 , pp. 701-704
    • Dill, K.A.1
  • 15
    • 0028334097 scopus 로고
    • Decomposition of the free-energy of a system in terms of specific interactions - Implications for theoretical and experimental studies
    • A.E. Mark, and W.F. van Gunsteren Decomposition of the free-energy of a system in terms of specific interactions - implications for theoretical and experimental studies J. Mol. Biol. 240 1994 167 176
    • (1994) J. Mol. Biol. , vol.240 , pp. 167-176
    • Mark, A.E.1    Van Gunsteren, W.F.2
  • 16
    • 77950022453 scopus 로고    scopus 로고
    • Non-additivity of functional group contributions in protein ligand binding: A comprehensive study by crystallography and isothermal titration calorimetry
    • B. Baum et al. Non-additivity of functional group contributions in protein ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry J. Mol. Biol. 397 2010 1042 1054
    • (2010) J. Mol. Biol. , vol.397 , pp. 1042-1054
    • Baum, B.1
  • 17
    • 80052398418 scopus 로고    scopus 로고
    • Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case
    • M.N. Ucisik et al. Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case J. Chem. Phys. 135 2011 085101
    • (2011) J. Chem. Phys. , vol.135 , pp. 085101
    • Ucisik, M.N.1
  • 19
    • 80055081145 scopus 로고    scopus 로고
    • How fast-folding proteins fold
    • K. Lindorff-Larsen et al. How fast-folding proteins fold Science 334 2011 517 520
    • (2011) Science , vol.334 , pp. 517-520
    • Lindorff-Larsen, K.1
  • 20
    • 84863775602 scopus 로고    scopus 로고
    • Refinement of protein structure homology models via long, all-atom molecular dynamics simulations
    • A. Raval et al. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations Proteins 80 2012 2071 2079
    • (2012) Proteins , vol.80 , pp. 2071-2079
    • Raval, A.1
  • 21
    • 84962424862 scopus 로고    scopus 로고
    • New universal solvation model and comparison of the accuracy of the SM5.42R, SM5.43R, C-PCM, D-PCM, and IEF-PCM continuum solvation models for aqueous and organic solvation free energies and for vapor pressures
    • J.D. Thompson et al. New universal solvation model and comparison of the accuracy of the SM5.42R, SM5.43R, C-PCM, D-PCM, and IEF-PCM continuum solvation models for aqueous and organic solvation free energies and for vapor pressures J. Phys. Chem. A 108 2004 6532 6542
    • (2004) J. Phys. Chem. A , vol.108 , pp. 6532-6542
    • Thompson, J.D.1
  • 22
    • 67649458222 scopus 로고    scopus 로고
    • Hydration free energies of amino acids: Why side chain analog data are not enough
    • G. Konig, and S. Boresch Hydration free energies of amino acids: why side chain analog data are not enough J. Phys. Chem. B 113 2009 8967 8974
    • (2009) J. Phys. Chem. B , vol.113 , pp. 8967-8974
    • Konig, G.1    Boresch, S.2
  • 23
    • 0348031808 scopus 로고
    • 2O)(N), N = 1-6. 2. Analysis of many-body interactions
    • 2O)(N), N = 1-6. 2. Analysis of many-body interactions J. Chem. Phys. 100 1994 7523 7534
    • (1994) J. Chem. Phys. , vol.100 , pp. 7523-7534
    • Xantheas, S.S.1
  • 24
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • W.L. Jorgensen et al. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1
  • 25
    • 1242346370 scopus 로고
    • The missing term in effective pair potentials
    • H.J.C. Berendsen et al. The missing term in effective pair potentials J. Phys. Chem. US 91 1987 6269 6271
    • (1987) J. Phys. Chem. US , vol.91 , pp. 6269-6271
    • Berendsen, H.J.C.1
  • 26
    • 84873641161 scopus 로고    scopus 로고
    • A critical assessment of two-body and three-body interactions in water
    • G.R. Medders et al. A critical assessment of two-body and three-body interactions in water J. Chem. Theory Comput. 9 2013 1103 1114
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 1103-1114
    • Medders, G.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.