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Volumn 80, Issue 3, 2012, Pages 683-690

Distance-dependent atomic knowledge-based force in protein fold recognition

Author keywords

3D structure; Decoy set; Interatomic force; Knowledge based potential; Score function

Indexed keywords

ARTICLE; ATOM; ENERGY; FORCE; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 84856778743     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24011     Document Type: Article
Times cited : (7)

References (53)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern folding of protein chains
    • Anfisen CB. Principles that govern folding of protein chains. Science 1973; 181: 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfisen, C.B.1
  • 3
    • 84988053694 scopus 로고
    • An all atom force-field for simulations of proteins and nucleic-acids
    • Weiner SJ, Kollman PA, Nguyen DT, Case DA. An all atom force-field for simulations of proteins and nucleic-acids. J Comput Chem 1986; 7: 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
  • 4
    • 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, Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 2006; 65: 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
  • 7
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen WL, Maxwell DS, 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 1996; 118: 11225-11236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 8
    • 84856776838 scopus 로고    scopus 로고
    • Knowledge-based potentials in protein fold recognition
    • Mirzaie M, Sadeghi M. Knowledge-based potentials in protein fold recognition. J Paramed Sci 2010; 1: 65-75.
    • (2010) J Paramed Sci , vol.1 , pp. 65-75
    • Mirzaie, M.1    Sadeghi, M.2
  • 9
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
    • Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromole 1985; 18: 534-552.
    • (1985) Macromole , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 10
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of native protein structures using atom-atom contact scoring
    • McConkey BJ, Sobolev V, Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci USA 2003; 100: 3215.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 3215
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 12
    • 0034646196 scopus 로고    scopus 로고
    • Environment-dependent residue contact energies for proteins
    • Zhang C, Kim SH. Environment-dependent residue contact energies for proteins. Proc Natl Acad Sci USA 2000; 97: 2550.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 2550
    • Zhang, C.1    Kim, S.H.2
  • 13
    • 42449129569 scopus 로고    scopus 로고
    • Information and discrimination in pairwise contact potentials
    • Solis AD, Rackovsky S. Information and discrimination in pairwise contact potentials. Proteins 2008; 71: 1071-1087.
    • (2008) Proteins , vol.71 , pp. 1071-1087
    • Solis, A.D.1    Rackovsky, S.2
  • 14
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge based mean force and protein folding. An approach to the computational determination of protein structures
    • Sippl MJ. Boltzmann's principle, knowledge based mean force and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 1993; 7: 473-501.
    • (1993) J Comput Aided Mol Des , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 15
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with nonlocal atomic interaction energy
    • Melo F, Feytmans E. Assessing protein structures with nonlocal atomic interaction energy. J Mol Biol 1998; 277: 1141-1152.
    • (1998) J Mol Biol , vol.277 , pp. 1141-1152
    • Melo, F.1    Feytmans, E.2
  • 16
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: an approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force: an approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990; 213: 859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 17
    • 0034308163 scopus 로고    scopus 로고
    • Distance dependent, pair potential for protein folding: results from linear optimization
    • Tobi D, Elber R. Distance dependent, pair potential for protein folding: results from linear optimization. Proteins 2000; 41: 40-56.
    • (2000) Proteins , vol.41 , pp. 40-56
    • Tobi, D.1    Elber, R.2
  • 18
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature 1992; 358: 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 19
    • 0032488962 scopus 로고    scopus 로고
    • An all atom distance dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J. An all atom distance dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998; 275: 895-916.
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 20
    • 0035882533 scopus 로고    scopus 로고
    • A distance dependent atomic knowledge based potential for improved protein structure selection
    • Lu H, Skolnick J. A distance dependent atomic knowledge based potential for improved protein structure selection. Proteins 2001; 44: 223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 21
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • Melo F, Feytmans E. Novel knowledge-based mean force potential at atomic level. J Mol Biol 1997; 267: 207.
    • (1997) J Mol Biol , vol.267 , pp. 207
    • Melo, F.1    Feytmans, E.2
  • 22
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure derived potentials of mean force for structure selection and stability prediction
    • Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 23
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • Chi Zhang, Song Liu, Hongyi Zhou, Yaoqi Zhou. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004; 13: 400-411.
    • (2004) Protein Sci , vol.13 , pp. 400-411
    • Chi, Z.1    Song, L.2    Hongyi, Z.3    Yaoqi, Z.4
  • 24
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006; 15: 2407-2524.
    • (2006) Protein Sci , vol.15 , pp. 2407-2524
    • Shen, M.1    Sali, A.2
  • 25
    • 35348892593 scopus 로고    scopus 로고
    • A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    • Ferrada E, Vergara IA, Melo F. A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations. Cell Biochem Biophys 2007; 49: 111-124.
    • (2007) Cell Biochem Biophys , vol.49 , pp. 111-124
    • Ferrada, E.1    Vergara, I.A.2    Melo, F.3
  • 26
    • 70349448457 scopus 로고    scopus 로고
    • A distance dependent atomic knowledge based potential and force for discrimination of native structures from decoys
    • Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M. A distance dependent atomic knowledge based potential and force for discrimination of native structures from decoys. Proteins 2009; 77: 454-463.
    • (2009) Proteins , vol.77 , pp. 454-463
    • Mirzaie, M.1    Eslahchi, C.2    Pezeshk, H.3    Sadeghi, M.4
  • 27
    • 0026009212 scopus 로고
    • Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions
    • Rooman MJ, Kocher JPA, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol 1991; 211: 961-979.
    • (1991) J Mol Biol , vol.211 , pp. 961-979
    • Rooman, M.J.1    Kocher, J.P.A.2    Wodak, S.J.3
  • 28
    • 19544371352 scopus 로고    scopus 로고
    • A consistent set of statistical potentials for quantifying local side-chain and backbone interactions
    • Fang Q, Shortle D. A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 2005; 60: 90.
    • (2005) Proteins , vol.60 , pp. 90
    • Fang, Q.1    Shortle, D.2
  • 29
    • 0015244817 scopus 로고
    • Empirical protein energy maps
    • Pohl FM. Empirical protein energy maps. Nat New Biol 1971; 234: 277.
    • (1971) Nat New Biol , vol.234 , pp. 277
    • Pohl, F.M.1
  • 30
    • 0041319042 scopus 로고    scopus 로고
    • The origin and extent of coarse-grained regularities in protein internal packing
    • Bagci Z, Kloczkowski A, Jernigan RL, Bahar I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins 2003; 53: 56-67.
    • (2003) Proteins , vol.53 , pp. 56-67
    • Bagci, Z.1    Kloczkowski, A.2    Jernigan, R.L.3    Bahar, I.4
  • 31
    • 1842454935 scopus 로고    scopus 로고
    • Orientational potentials extracted from protein structures improves native fold recognition
    • Buchete NV, Straub JE, Thirumalai D. Orientational potentials extracted from protein structures improves native fold recognition. Protein Sci 2004; 13: 862.
    • (2004) Protein Sci , vol.13 , pp. 862
    • Buchete, N.V.1    Straub, J.E.2    Thirumalai, D.3
  • 32
    • 1942423584 scopus 로고    scopus 로고
    • Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis
    • Buchete NV, Straub JE, Thirumalai D. Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. J Mol Graph Model 2004; 22: 441.
    • (2004) J Mol Graph Model , vol.22 , pp. 441
    • Buchete, N.V.1    Straub, J.E.2    Thirumalai, D.3
  • 33
    • 34548064535 scopus 로고    scopus 로고
    • Orientation-dependent potential of mean force for protein folding
    • Mukherjee A, Bhimalapuram P, Bagchi B. Orientation-dependent potential of mean force for protein folding. J Chem Phys 2005; 123: 014901.
    • (2005) J Chem Phys , vol.123 , pp. 014901
    • Mukherjee, A.1    Bhimalapuram, P.2    Bagchi, B.3
  • 34
    • 4344598766 scopus 로고    scopus 로고
    • Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction
    • Misura KM, Morozov AV, Baker D. Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. J Mol Biol 2004; 342: 651-664.
    • (2004) J Mol Biol , vol.342 , pp. 651-664
    • Misura, K.M.1    Morozov, A.V.2    Baker, D.3
  • 35
    • 22944468214 scopus 로고    scopus 로고
    • How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
    • Miyazawa S, Jernigan RL. How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins? J Chem Phys 2005; 122: 024901.
    • (2005) J Chem Phys , vol.122 , pp. 024901
    • Miyazawa, S.1    Jernigan, R.L.2
  • 36
    • 34250829219 scopus 로고    scopus 로고
    • OPUS-Ca: a knowledge based potential function requiring only Calpha positions
    • Wu Y, Lu M, Chen M, Li J, Ma J. OPUS-Ca: a knowledge based potential function requiring only Calpha positions. Protein Sci 2007; 16: 1449-1463.
    • (2007) Protein Sci , vol.16 , pp. 1449-1463
    • Wu, Y.1    Lu, M.2    Chen, M.3    Li, J.4    Ma, J.5
  • 37
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995; 5: 229-235.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 38
    • 0026761547 scopus 로고
    • Folding protein alpha-carbon chains into compact forms by Monte Carlo methods
    • Covell DG. Folding protein alpha-carbon chains into compact forms by Monte Carlo methods. Proteins 1992; 14: 409-420.
    • (1992) Proteins , vol.14 , pp. 409-420
    • Covell, D.G.1
  • 39
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: statistical potential and genetic algorithms
    • Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993; 2: 762-785.
    • (1993) Protein Sci , vol.2 , pp. 762-785
    • Sun, S.1
  • 40
    • 0030054951 scopus 로고    scopus 로고
    • Delaunay tessellation of proteins:Four body nearest neighbor propensities of amino acid residues
    • Singh RK, Tropsha A, Vaisman II. Delaunay tessellation of proteins:Four body nearest neighbor propensities of amino acid residues. J Comput Biol 1996; 3: 213-221.
    • (1996) J Comput Biol , vol.3 , pp. 213-221
    • Singh, R.K.1    Tropsha, A.2    Vaisman, I.I.3
  • 41
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi body potentials based on Delaunay tessellation and their application insequence structure alignment
    • Munson PJ, Singh RK. Statistical significance of hierarchical multi body potentials based on Delaunay tessellation and their application insequence structure alignment. Protein Sci 1997; 6: 1467-1481.
    • (1997) Protein Sci , vol.6 , pp. 1467-1481
    • Munson, P.J.1    Singh, R.K.2
  • 44
    • 34250886494 scopus 로고    scopus 로고
    • Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models
    • Ferrada E, Melo F. Nonbonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models. Protein Sci 2007; 16: 1410-1421.
    • (2007) Protein Sci , vol.16 , pp. 1410-1421
    • Ferrada, E.1    Melo, F.2
  • 45
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996; 258: 367-392.
    • (1996) J Mol Biol , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 46
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 47
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • Simons KT, Ruczinski I, Kooperberg C, Fox B A, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999; 34: 82-95.
    • (1999) Proteins , vol.34 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 48
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structures using a hierarchical approach
    • Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol 2000; 300: 171-185.
    • (2000) J Mol Biol , vol.300 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 49
    • 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, Levitt M. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol 2003; 329: 159-174.
    • (2003) J Mol Biol , vol.329 , pp. 159-174
    • Keasar, C.1    Levitt, M.2
  • 50
    • 0141978673 scopus 로고    scopus 로고
    • Comparative protein structure mideling by iterative alighnment, model building and model assessment
    • John B, Sali A. Comparative protein structure mideling by iterative alighnment, model building and model assessment. Nucleic Acid Res 2003; 31: 3982-3992.
    • (2003) Nucleic Acid Res , vol.31 , pp. 3982-3992
    • John, B.1    Sali, A.2
  • 52
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007; 5: 17.
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 53
    • 78149453870 scopus 로고    scopus 로고
    • A novel side chain orientation dependent potential derived from random walk reference state for protein fold selection and structure prediction
    • Zhang J, Zhang Y. A novel side chain orientation dependent potential derived from random walk reference state for protein fold selection and structure prediction. PloS ONE 2010; 5: e15386.
    • (2010) PloS ONE , vol.5
    • Zhang, J.1    Zhang, Y.2


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