메뉴 건너뛰기




Volumn 15, Issue 6, 2007, Pages 727-740

Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; ENERGY; ENTROPY; HYDRATION; HYDROPHOBICITY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SOLVATION; THERMAL ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 34249892163     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2007.05.004     Document Type: Article
Times cited : (48)

References (96)
  • 1
    • 36749107785 scopus 로고
    • Molecular-dynamics simulations at constant pressure and-or temperature
    • Andersen H.C. Molecular-dynamics simulations at constant pressure and-or temperature. J. Chem. Phys. 72 (1980) 2384-2393
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 2
    • 36749115010 scopus 로고
    • The role of long ranged forces in determining the structure and properties of liquid water
    • Andrea T.A., Swope W.C., and Andersen H.C. The role of long ranged forces in determining the structure and properties of liquid water. J. Chem. Phys. 79 (1983) 4576-4584
    • (1983) J. Chem. Phys. , vol.79 , pp. 4576-4584
    • Andrea, T.A.1    Swope, W.C.2    Andersen, H.C.3
  • 3
    • 0015859467 scopus 로고
    • Principles that govern folding of protein chains
    • Anfinsen C.B. Principles that govern folding of protein chains. Science 181 (1973) 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 4
    • 0000180763 scopus 로고
    • Temperature-dependence of the hydrophobic interaction in protein folding
    • Baldwin R.L. Temperature-dependence of the hydrophobic interaction in protein folding. Proc. Natl. Acad. Sci. USA 83 (1986) 8069-8072
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 8069-8072
    • Baldwin, R.L.1
  • 5
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman B. (Ed), D. Reidel Publishing Company, Dordrecht, The Netherlands
    • Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B. (Ed). Intermolecular Forces (1981), D. Reidel Publishing Company, Dordrecht, The Netherlands 331-342
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    van Gunsteren, W.F.3    Hermans, J.4
  • 6
    • 0345827706 scopus 로고    scopus 로고
    • ProVal: a protein-scoring function for the selection of native and near-native folds
    • Berglund A., Head R.D., Welsh E.A., and Marshall G.R. ProVal: a protein-scoring function for the selection of native and near-native folds. Proteins 54 (2004) 289-302
    • (2004) Proteins , vol.54 , pp. 289-302
    • Berglund, A.1    Head, R.D.2    Welsh, E.A.3    Marshall, G.R.4
  • 9
    • 26944481188 scopus 로고    scopus 로고
    • Interfaces and the driving force of hydrophobic assembly
    • Chandler D. Interfaces and the driving force of hydrophobic assembly. Nature 437 (2005) 640-647
    • (2005) Nature , vol.437 , pp. 640-647
    • Chandler, D.1
  • 10
    • 0000782351 scopus 로고    scopus 로고
    • Development of polarizable water force fields for phase equilibrium calculations
    • Chen B., Xing J.H., and Siepmann J.I. Development of polarizable water force fields for phase equilibrium calculations. J. Phys. Chem. B 104 (2000) 2391-2401
    • (2000) J. Phys. Chem. B , vol.104 , pp. 2391-2401
    • Chen, B.1    Xing, J.H.2    Siepmann, J.I.3
  • 11
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible surface area in proteins
    • Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature 248 (1974) 338-339
    • (1974) Nature , vol.248 , pp. 338-339
    • Chothia, C.1
  • 12
    • 85047691965 scopus 로고
    • Self-consistent field-theory of solvent effects representation by continuum models-introduction of desolvation contribution
    • Constanciel R., and Contreras R. Self-consistent field-theory of solvent effects representation by continuum models-introduction of desolvation contribution. Theor. Chim. Acta 65 (1984) 1-11
    • (1984) Theor. Chim. Acta , vol.65 , pp. 1-11
    • Constanciel, R.1    Contreras, R.2
  • 15
    • 33744906496 scopus 로고    scopus 로고
    • A new generation of statistical potentials for proteins
    • Dehouck Y., Gilis D., and Rooman M. A new generation of statistical potentials for proteins. Biophys. J. 90 (2006) 4010-4017
    • (2006) Biophys. J. , vol.90 , pp. 4010-4017
    • Dehouck, Y.1    Gilis, D.2    Rooman, M.3
  • 16
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill K.A. Dominant forces in protein folding. Biochemistry 29 (1990) 7133-7155
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 17
    • 0037079585 scopus 로고    scopus 로고
    • Identifying native-like protein structures using physics-based potentials
    • Dominy B.N., and Brooks C.L. Identifying native-like protein structures using physics-based potentials. J. Comput. Chem. 23 (2002) 147-160
    • (2002) J. Comput. Chem. , vol.23 , pp. 147-160
    • Dominy, B.N.1    Brooks, C.L.2
  • 18
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D., and McLachlan A.D. Solvation energy in protein folding and binding. Nature 319 (1986) 199-203
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 19
    • 0035327508 scopus 로고    scopus 로고
    • Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins
    • Fain B., Xia Y., and Levitt M. Determination of optimal Chebyshev-expanded hydrophobic discrimination function for globular proteins. IBM Journal Research and Development 45 (2001) 525-532
    • (2001) IBM Journal Research and Development , vol.45 , pp. 525-532
    • Fain, B.1    Xia, Y.2    Levitt, M.3
  • 20
    • 0036836611 scopus 로고    scopus 로고
    • Evaluating CASP4 predictions with physical energy functions
    • Feig M., and Brooks C.L. Evaluating CASP4 predictions with physical energy functions. Proteins 49 (2002) 232-245
    • (2002) Proteins , vol.49 , pp. 232-245
    • Feig, M.1    Brooks, C.L.2
  • 21
    • 0036681394 scopus 로고    scopus 로고
    • Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model
    • Felts A.K., Gallicchio E., Wallqvist A., and Levy R.M. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model. Proteins 48 (2002) 404-422
    • (2002) Proteins , vol.48 , pp. 404-422
    • Felts, A.K.1    Gallicchio, E.2    Wallqvist, A.3    Levy, R.M.4
  • 22
    • 1442330396 scopus 로고    scopus 로고
    • AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
    • Gallicchio E., and Levy R.M. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. 25 (2004) 479-499
    • (2004) J. Comput. Chem. , vol.25 , pp. 479-499
    • Gallicchio, E.1    Levy, R.M.2
  • 23
    • 0037022662 scopus 로고    scopus 로고
    • α-helical stabilization by side chain shielding of backbone hydrogen bonds
    • Garcia A.E., and Sanbonmatsu K.Y. α-helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. USA 99 (2002) 2782-2787
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 2782-2787
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 24
    • 0034560338 scopus 로고    scopus 로고
    • Discrimination of near-native protein structures from misfolded models by empirical free energy functions
    • Gatchell D.W., Dennis S., and Vajda S. Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 41 (2000) 518-534
    • (2000) Proteins , vol.41 , pp. 518-534
    • Gatchell, D.W.1    Dennis, S.2    Vajda, S.3
  • 25
    • 0028823713 scopus 로고
    • Structures of protein complexes by multidimensional heteronuclear magnetic-resonance spectroscopy
    • Gronenborn A.M., and Clore G.M. Structures of protein complexes by multidimensional heteronuclear magnetic-resonance spectroscopy. Crit. Rev. Biochem. Mol. Biol. 30 (1995) 351
    • (1995) Crit. Rev. Biochem. Mol. Biol. , vol.30 , pp. 351
    • Gronenborn, A.M.1    Clore, G.M.2
  • 26
    • 0001308921 scopus 로고
    • A rapid approximation to the solvent accessible surface areas of atoms
    • Hasel W., Hendrickson T.F., and Still W.C. A rapid approximation to the solvent accessible surface areas of atoms. Tetrahdron Computer Methodology 1 (1988) 103-116
    • (1988) Tetrahdron Computer Methodology , vol.1 , pp. 103-116
    • Hasel, W.1    Hendrickson, T.F.2    Still, W.C.3
  • 27
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins G.D., Cramer C.J., and Truhlar D.G. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246 (1995) 122-129
    • (1995) Chem. Phys. Lett. , vol.246 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 28
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • Hawkins G.D., Cramer C.J., and Truhlar D.G. Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100 (1996) 19824-19839
    • (1996) J. Phys. Chem. , vol.100 , pp. 19824-19839
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 29
    • 0030822464 scopus 로고    scopus 로고
    • Differences in hydration structure near hydrophobic and hydrophilic amino acids
    • Head-Gordon T., Sorenson J.M., Pertsemlidis A., and Glaeser R.M. Differences in hydration structure near hydrophobic and hydrophilic amino acids. Biophys. J. 73 (1997) 2106-2115
    • (1997) Biophys. J. , vol.73 , pp. 2106-2115
    • Head-Gordon, T.1    Sorenson, J.M.2    Pertsemlidis, A.3    Glaeser, R.M.4
  • 30
    • 0026505184 scopus 로고
    • Evaluation of protein models by atomic solvation preference
    • Holm L., and Sander C. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225 (1992) 93-105
    • (1992) J. Mol. Biol. , vol.225 , pp. 93-105
    • Holm, L.1    Sander, C.2
  • 32
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple amber force fields and development of improved protein backbone parameters
    • Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., and Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65 (2006) 712-725
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 33
    • 3142680776 scopus 로고    scopus 로고
    • Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction
    • Hsieh M.J., and Luo R. Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins 56 (2004) 475-486
    • (2004) Proteins , vol.56 , pp. 475-486
    • Hsieh, M.J.1    Luo, R.2
  • 34
    • 0033404370 scopus 로고    scopus 로고
    • Solution X-ray scattering as a probe of hydration-dependent structuring of aqueous solutions
    • Hura G., Sorenson J.M., Glaeser R.M., and Head-Gordon T. Solution X-ray scattering as a probe of hydration-dependent structuring of aqueous solutions. Perspect. Drug Discov. Des. 17 (1999) 97-118
    • (1999) Perspect. Drug Discov. Des. , vol.17 , pp. 97-118
    • Hura, G.1    Sorenson, J.M.2    Glaeser, R.M.3    Head-Gordon, T.4
  • 35
    • 84906391926 scopus 로고
    • Temperature and size dependence for Monte-Carlo simulations of Tip4p water
    • Jorgensen W.L., and Madura J.D. Temperature and size dependence for Monte-Carlo simulations of Tip4p water. Mol. Phys. 56 (1985) 1381-1392
    • (1985) Mol. Phys. , vol.56 , pp. 1381-1392
    • Jorgensen, W.L.1    Madura, J.D.2
  • 37
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. 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    Maxwell, D.S.2    Tirado-Rives, J.3
  • 38
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski G.A., Friesner R.A., Tirado-Rives J., and Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105 (2001) 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 39
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14 (1959) 1-63
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 40
    • 0038708222 scopus 로고    scopus 로고
    • A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics
    • Keasar C., and Levitt M. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J. Mol. Biol. 329 (2003) 159-174
    • (2003) J. Mol. Biol. , vol.329 , pp. 159-174
    • Keasar, C.1    Levitt, M.2
  • 41
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • Lazaridis T., and Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J. Mol. Biol. 288 (1999) 477-487
    • (1999) J. Mol. Biol. , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 42
    • 0015222647 scopus 로고
    • Interpretation of protein structures-estimation of static accessibility
    • Lee B., and Richards F.M. Interpretation of protein structures-estimation of static accessibility. J. Mol. Biol. 55 (1971) 379
    • (1971) J. Mol. Biol. , vol.55 , pp. 379
    • Lee, B.1    Richards, F.M.2
  • 43
    • 0034788323 scopus 로고    scopus 로고
    • Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction
    • Lee M.R., and Kollman P.A. Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. Structure 9 (2001) 905-916
    • (2001) Structure , vol.9 , pp. 905-916
    • Lee, M.R.1    Kollman, P.A.2
  • 44
    • 2442480826 scopus 로고    scopus 로고
    • Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
    • Lee M.C., and Duan Y. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55 (2004) 620-634
    • (2004) Proteins , vol.55 , pp. 620-634
    • Lee, M.C.1    Duan, Y.2
  • 45
    • 0035914481 scopus 로고    scopus 로고
    • Molecular dynamics in the endgame of protein structure prediction
    • Lee M.R., Tsai J., Baker D., and Kollman P.A. Molecular dynamics in the endgame of protein structure prediction. J. Mol. Biol. 313 (2001) 417-430
    • (2001) J. Mol. Biol. , vol.313 , pp. 417-430
    • Lee, M.R.1    Tsai, J.2    Baker, D.3    Kollman, P.A.4
  • 46
    • 33646887390 scopus 로고
    • On the limited memory Bfgs method for large-scale optimization
    • Liu D.C., and Nocedal J. On the limited memory Bfgs method for large-scale optimization. Math. Program. 45 (1989) 503-528
    • (1989) Math. Program. , vol.45 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 47
    • 24344448662 scopus 로고    scopus 로고
    • Observation of a dewetting transition in the collapse of the melittin tetramer
    • Liu P., Huang X.H., Zhou R.H., and Berne B.J. Observation of a dewetting transition in the collapse of the melittin tetramer. Nature 437 (2005) 159-162
    • (2005) Nature , vol.437 , pp. 159-162
    • Liu, P.1    Huang, X.H.2    Zhou, R.H.3    Berne, B.J.4
  • 49
    • 0000020246 scopus 로고    scopus 로고
    • A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
    • Mahoney M.W., and Jorgensen W.L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112 (2000) 8910-8922
    • (2000) J. Chem. Phys. , vol.112 , pp. 8910-8922
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 50
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of native protein structures using atom-atom contact scoring
    • McConkey B.J., Sobolev V., and Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc. Natl. Acad. Sci. USA 100 (2003) 3215-3220
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3215-3220
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 51
    • 0034864528 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms for molecular simulations of biopolymers
    • Mitsutake A., Sugita Y., and Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 60 (2001) 96-123
    • (2001) Biopolymers , vol.60 , pp. 96-123
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 52
    • 5944250450 scopus 로고
    • Energy parameters in polypeptides. 7. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen-bond interactions, and intrinsic torsional potentials for naturally occurring amino-acids
    • Momany F.A., Mcguire R.F., Burgess A.W., and Scheraga H.A. Energy parameters in polypeptides. 7. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen-bond interactions, and intrinsic torsional potentials for naturally occurring amino-acids. J. Phys. Chem. 79 (1975) 2361-2381
    • (1975) J. Phys. Chem. , vol.79 , pp. 2361-2381
    • Momany, F.A.1    Mcguire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 53
    • 34548064535 scopus 로고    scopus 로고
    • Orientation-dependent potential of mean force for protein folding
    • Mukherjee A., Bhimalapuram P., and Bagchi B. Orientation-dependent potential of mean force for protein folding. J. Chem. Phys. 123 (2005) 14901
    • (2005) J. Chem. Phys. , vol.123 , pp. 14901
    • Mukherjee, A.1    Bhimalapuram, P.2    Bagchi, B.3
  • 54
    • 30744462062 scopus 로고    scopus 로고
    • Protein structure evaluation using an all-atom energy based empirical scoring function
    • Narang P., Bhushan K., Bose S., and Jayaram B. Protein structure evaluation using an all-atom energy based empirical scoring function. J. Biomol. Struct. Dyn. 23 (2006) 385-406
    • (2006) J. Biomol. Struct. Dyn. , vol.23 , pp. 385-406
    • Narang, P.1    Bhushan, K.2    Bose, S.3    Jayaram, B.4
  • 55
    • 33845550595 scopus 로고
    • Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen-bond interactions for the naturally-occurring amino-acids
    • Nemethy G., Pottle M.S., and Scheraga H.A. Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen-bond interactions for the naturally-occurring amino-acids. J. Phys. Chem. 87 (1983) 1883-1887
    • (1983) J. Phys. Chem. , vol.87 , pp. 1883-1887
    • Nemethy, G.1    Pottle, M.S.2    Scheraga, H.A.3
  • 56
    • 0021691918 scopus 로고
    • An analysis of incorrectly folded protein models-implications for structure predictions
    • Novotny J., Bruccoleri R., and Karplus M. An analysis of incorrectly folded protein models-implications for structure predictions. J. Mol. Biol. 177 (1984) 787-818
    • (1984) J. Mol. Biol. , vol.177 , pp. 787-818
    • Novotny, J.1    Bruccoleri, R.2    Karplus, M.3
  • 57
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized Born model suitable for macromolecules
    • Onufriev A., Bashford D., and Case D.A. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 104 (2000) 3712-3720
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 58
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • Onufriev A., Bashford D., and Case D.A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55 (2004) 383-394
    • (2004) Proteins , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 59
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
    • Pande V.S., and Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA 96 (1999) 9062-9067
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 60
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park B., and Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258 (1996) 367-392
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 61
    • 0029746155 scopus 로고    scopus 로고
    • Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid
    • Pertsemlidis A., Saxena A.M., Soper A.K., Head-Gordon T., and Glaeser R.M. Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc. Natl. Acad. Sci. USA 93 (1996) 10769-10774
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 10769-10774
    • Pertsemlidis, A.1    Saxena, A.M.2    Soper, A.K.3    Head-Gordon, T.4    Glaeser, R.M.5
  • 63
    • 0034486196 scopus 로고    scopus 로고
    • Free energy determinants of tertiary structure and the evaluation of protein models
    • Petrey D., and Honig B. Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci. 9 (2000) 2181-2191
    • (2000) Protein Sci. , vol.9 , pp. 2181-2191
    • Petrey, D.1    Honig, B.2
  • 64
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • Ponder J.W., and Case D.A. Force fields for protein simulations. Adv. Protein Chem. 66 (2003) 27-85
    • (2003) Adv. Protein Chem. , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 65
    • 36749120002 scopus 로고
    • Theory of hydrophobic effect
    • Pratt L.R., and Chandler D. Theory of hydrophobic effect. J. Chem. Phys. 67 (1977) 3683-3704
    • (1977) J. Chem. Phys. , vol.67 , pp. 3683-3704
    • Pratt, L.R.1    Chandler, D.2
  • 67
    • 0034831674 scopus 로고    scopus 로고
    • Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model
    • Rick S.W. Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model. J. Chem. Phys. 114 (2001) 2276-2283
    • (2001) J. Chem. Phys. , vol.114 , pp. 2276-2283
    • Rick, S.W.1
  • 68
    • 1942425662 scopus 로고    scopus 로고
    • A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums
    • Rick S.W. A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. J. Chem. Phys. 120 (2004) 6085-6093
    • (2004) J. Chem. Phys. , vol.120 , pp. 6085-6093
    • Rick, S.W.1
  • 69
    • 36448999850 scopus 로고
    • Dynamical fluctuating charge force-fields-application to liquid water
    • Rick S.W., Stuart S.J., and Berne B.J. Dynamical fluctuating charge force-fields-application to liquid water. J. Chem. Phys. 101 (1994) 6141-6156
    • (1994) J. Chem. Phys. , vol.101 , pp. 6141-6156
    • Rick, S.W.1    Stuart, S.J.2    Berne, B.J.3
  • 70
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction
    • Samudrala R., and Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci. 9 (2000) 1399-1401
    • (2000) Protein Sci. , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 72
    • 0026416668 scopus 로고
    • Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
    • Sharp K.A., Nicholls A., Fine R.F., and Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252 (1991) 106-109
    • (1991) Science , vol.252 , pp. 106-109
    • Sharp, K.A.1    Nicholls, A.2    Fine, R.F.3    Honig, B.4
  • 73
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen M.Y., and Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15 (2006) 2507-2524
    • (2006) Protein Sci. , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 74
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms-lysozyme and insulin
    • Shrake A., and Rupley J.A. Environment and exposure to solvent of protein atoms-lysozyme and insulin. J. Mol. Biol. 79 (1973) 351-371
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 75
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C., Strockbine B., and Roitberg A.E. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124 (2002) 11258-11259
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 76
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons K.T., Kooperberg C., Huang E., and Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268 (1997) 209-225
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 77
    • 0032612579 scopus 로고    scopus 로고
    • Ab initio protein structure prediction of CASP III targets using ROSETTA
    • Simons K.T., Bonneau R., Ruczinski I., and Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl. 3 (1999) 171-176
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 171-176
    • Simons, K.T.1    Bonneau, R.2    Ruczinski, I.3    Baker, D.4
  • 78
    • 27244454740 scopus 로고
    • Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H=O=C hydrogen-bonds from packing configurations
    • Sippl M.J., Nemethy G., and Scheraga H.A. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H=O=C hydrogen-bonds from packing configurations. J. Phys. Chem. 88 (1984) 6231-6233
    • (1984) J. Phys. Chem. , vol.88 , pp. 6231-6233
    • Sippl, M.J.1    Nemethy, G.2    Scheraga, H.A.3
  • 80
    • 0000866128 scopus 로고
    • Hydrophobic effect in protein folding and other noncovalent processes involving proteins
    • Spolar R.S., Ha J.H., and Record Jr. M.T. Hydrophobic effect in protein folding and other noncovalent processes involving proteins. Proc. Natl. Acad. Sci. USA 86 (1989) 8382-8385
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 8382-8385
    • Spolar, R.S.1    Ha, J.H.2    Record Jr., M.T.3
  • 81
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990) 6127-6129
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 82
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 83
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson J.M., Henchman R.H., and McCammon J.A. Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 86 (2004) 67-74
    • (2004) Biophys. J. , vol.86 , pp. 67-74
    • Swanson, J.M.1    Henchman, R.H.2    McCammon, J.A.3
  • 84
    • 0037078482 scopus 로고    scopus 로고
    • Hydrophobic interactions: an overview
    • ten Wolde P.R. Hydrophobic interactions: an overview. J. Phys. Condens. Matter 14 (2002) 9445-9460
    • (2002) J. Phys. Condens. Matter , vol.14 , pp. 9445-9460
    • ten Wolde, P.R.1
  • 85
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • Tsai J., Bonneau R., Morozov A.V., Kuhlman B., Rohl C.A., and Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53 (2003) 76-87
    • (2003) Proteins , vol.53 , pp. 76-87
    • Tsai, J.1    Bonneau, R.2    Morozov, A.V.3    Kuhlman, B.4    Rohl, C.A.5    Baker, D.6
  • 87
    • 0001290941 scopus 로고
    • Conformational energy calculations on polypeptides and proteins
    • Vasquez M., Nemethy G., and Scheraga H.A. Conformational energy calculations on polypeptides and proteins. Chem. Rev. 94 (1994) 2183-2239
    • (1994) Chem. Rev. , vol.94 , pp. 2183-2239
    • Vasquez, M.1    Nemethy, G.2    Scheraga, H.A.3
  • 88
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev Y.N., Almagro J.C., and Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 32 (1998) 399-413
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 89
    • 33744822783 scopus 로고    scopus 로고
    • Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms
    • Wagoner J.A., and Baker N.A. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc. Natl. Acad. Sci. USA 103 (2006) 8331-8336
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 8331-8336
    • Wagoner, J.A.1    Baker, N.A.2
  • 90
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J.M., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J. Comput. Chem. 21 (2000) 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 91
    • 4544355522 scopus 로고    scopus 로고
    • Improved protein structure selection using decoy-dependent discriminatory functions
    • Wang K., Fain B., Levitt M., and Samudrala R. Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct. Biol. 4 (2004) 8
    • (2004) BMC Struct. Biol. , vol.4 , pp. 8
    • Wang, K.1    Fain, B.2    Levitt, M.3    Samudrala, R.4
  • 92
    • 33645716062 scopus 로고    scopus 로고
    • Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
    • Wang Z.X., Zhang W., Wu C., Lei H.X., Cieplak P., and Duan Y. Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 27 (2006) 781-790
    • (2006) J. Comput. Chem. , vol.27 , pp. 781-790
    • Wang, Z.X.1    Zhang, W.2    Wu, C.3    Lei, H.X.4    Cieplak, P.5    Duan, Y.6
  • 94
    • 84988053694 scopus 로고
    • An all atom force-field for simulations of proteins and nucleic-acids
    • Weiner S.J., Kollman P.A., Nguyen D.T., and Case D.A. An all atom force-field for simulations of proteins and nucleic-acids. J. Comput. Chem. 7 (1986) 230-252
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 95
    • 33845977740 scopus 로고    scopus 로고
    • On side-chain conformational entropy of proteins
    • Zhang J.F., and Liu J.S. On side-chain conformational entropy of proteins. PLoS Comput. Biol. 2 (2006) 1586-1591
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 1586-1591
    • Zhang, J.F.1    Liu, J.S.2
  • 96
    • 0042921442 scopus 로고    scopus 로고
    • How well can we predict native contacts in proteins based on decoy structures and their energies?
    • Zhu J., Zhu Q.Q., Shi Y.Y., and Liu H.Y. How well can we predict native contacts in proteins based on decoy structures and their energies?. Proteins 52 (2003) 598-608
    • (2003) Proteins , vol.52 , pp. 598-608
    • Zhu, J.1    Zhu, Q.Q.2    Shi, Y.Y.3    Liu, H.Y.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.