메뉴 건너뛰기




Volumn 288, Issue 4, 1999, Pages 725-742

Prediction of protein tertiauy structure to low resolution: Performance for a large and structurally diverse test set

Author keywords

Global optimization; Metropolis criterion; Protein folding; Reduced model; Simulated annealing

Indexed keywords

PROTEIN;

EID: 0032588985     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2702     Document Type: Article
Times cited : (45)

References (26)
  • 3
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential - hydrophobic potential derived from X-ray structures of globular-proteins is able to identify native folds
    • Casari G., Sippl M. J. Structure-derived hydrophobic potential - hydrophobic potential derived from X-ray structures of globular-proteins is able to identify native folds. J. Mol. Biol. 224:1992;725-732.
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.J.2
  • 4
    • 0030203970 scopus 로고    scopus 로고
    • Evolutionary algorithms in computer-aided molecular design
    • Clark D. E., Westhead D. R. Evolutionary algorithms in computer-aided molecular design. J. Comput.-Aided Mol. Des. 10:1996;337-358.
    • (1996) J. Comput.-Aided Mol. Des. , vol.10 , pp. 337-358
    • Clark, D.E.1    Westhead, D.R.2
  • 5
    • 0029980527 scopus 로고    scopus 로고
    • Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions
    • Dandekar T., Argos P. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. J. Mol. Biol. 256:1996;645-660.
    • (1996) J. Mol. Biol. , vol.256 , pp. 645-660
    • Dandekar, T.1    Argos, P.2
  • 6
    • 0030779795 scopus 로고    scopus 로고
    • Applying experimental data to protein fold prediction with the genetic algorithm
    • Dandekar T., Argos P. Applying experimental data to protein fold prediction with the genetic algorithm. Protein Eng. 10:1997;877-893.
    • (1997) Protein Eng. , vol.10 , pp. 877-893
    • Dandekar, T.1    Argos, P.2
  • 7
    • 0345019895 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein folds
    • Dandekar T., Konig R. Computational methods for the prediction of protein folds. Biochim. Biophys. Acta. 1343:1997;1-15.
    • (1997) Biochim. Biophys. Acta , vol.1343 , pp. 1-15
    • Dandekar, T.1    Konig, R.2
  • 8
    • 0031559499 scopus 로고    scopus 로고
    • Equilibrium states of rigid bodies with multiple interaction sites: Application to protein helices
    • Erman B., Bahar I., Jemigan R. L. Equilibrium states of rigid bodies with multiple interaction sites: application to protein helices. J. Chem. Phys. 107:1997;2046-2059.
    • (1997) J. Chem. Phys. , vol.107 , pp. 2046-2059
    • Erman, B.1    Bahar, I.2    Jemigan, R.L.3
  • 10
    • 0000335209 scopus 로고
    • Hierarchical algorithm for computer modeling of protein tertiary structure-folding of myoglobin to 6. 2 Ångstrom resolution
    • Gunn J. R., Monge A., Friesner R. A., Marshall C. H. Hierarchical algorithm for computer modeling of protein tertiary structure-folding of myoglobin to 6. 2 Ångstrom resolution. J. Phys. Chem. 98:1994;702-711.
    • (1994) J. Phys. Chem. , vol.98 , pp. 702-711
    • Gunn, J.R.1    Monge, A.2    Friesner, R.A.3    Marshall, C.H.4
  • 11
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U., Sander C. Enlarged representative set of protein structures. Protein Sci. 3:1994;522-524.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 12
    • 0029871791 scopus 로고    scopus 로고
    • Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
    • Huang E. S., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J. Mol. Biol. 257:1996;716-725.
    • (1996) J. Mol. Biol. , vol.257 , pp. 716-725
    • Huang, E.S.1    Subbiah, S.2    Tsai, J.3    Levitt, M.4
  • 13
    • 84986532547 scopus 로고
    • Conserving energy during molecular-dynamics simulations of water, proteins, and proteins in water
    • Kitchen D. B., Hirata F., Westbrook J. D., Levy R., Kofke D., Yarmush M. Conserving energy during molecular-dynamics simulations of water, proteins, and proteins in water. J. Comput. Chem. 11:1990;1169-1180.
    • (1990) J. Comput. Chem. , vol.11 , pp. 1169-1180
    • Kitchen, D.B.1    Hirata, F.2    Westbrook, J.D.3    Levy, R.4    Kofke, D.5    Yarmush, M.6
  • 14
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z., Scheraga H. A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl Acad. Sci. USA. 84:1987;6611-6615.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 15
    • 0028955505 scopus 로고
    • Predicting the helix packing of globular-proteins by self- correcting distance geometry
    • Mumenthaler C., Braun W. Predicting the helix packing of globular-proteins by self- correcting distance geometry. Protein Sci. 4:1995;863-871.
    • (1995) Protein Sci. , vol.4 , pp. 863-871
    • Mumenthaler, C.1    Braun, W.2
  • 16
    • 0030634582 scopus 로고    scopus 로고
    • Tertiary structure prediction using mean-force potentials and internal energy functions: Successful prediction for coiled-coil
    • Odonoghue S. I., Nilges M. Tertiary structure prediction using mean-force potentials and internal energy functions: successful prediction for coiled-coil. Fold. Design. 2:1997;S47-S52.
    • (1997) Fold. Design , vol.2
    • Odonoghue, S.I.1    Nilges, M.2
  • 17
    • 0032571390 scopus 로고    scopus 로고
    • Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
    • Ortiz A. R., Kolinski A., Skolnick J. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J. Mol. Biol. 277:1998;419-448.
    • (1998) J. Mol. Biol. , vol.277 , pp. 419-448
    • Ortiz, A.R.1    Kolinski, A.2    Skolnick, J.3
  • 18
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70 % accuracy
    • Rost B., Sander C. Prediction of protein secondary structure at better than 70 % accuracy. J. Mol. Biol. 232:1993;584-599.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 19
    • 0028300741 scopus 로고
    • Combining evolutionary information and neural networks to predict protein secondary structure
    • Rost B., Sander C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins: Struct. Funct. Genet. 19:1994;55-72.
    • (1994) Proteins: Struct. Funct. Genet. , vol.19 , pp. 55-72
    • Rost, B.1    Sander, C.2
  • 20
    • 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., 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
  • 21
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Skolnick J., Kolinski A., Ortiz A. R. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265:1997;217-241.
    • (1997) J. Mol. Biol. , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 23
    • 0033613919 scopus 로고    scopus 로고
    • A branch and bound algorithm for protein structure refinement from sparse NMR data sets
    • Standley D. M., Eyrich V. A., Felts A. K., Friesner R. A., McDermott A. E. A branch and bound algorithm for protein structure refinement from sparse NMR data sets. J. Mol. Biol. 285:1999;1689-1708.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1689-1708
    • Standley, D.M.1    Eyrich, V.A.2    Felts, A.K.3    Friesner, R.A.4    McDermott, A.E.5
  • 24
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still W. C., Tempczyk A., Hawley R. C., 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
  • 25
    • 0027503403 scopus 로고
    • Reduced representation model of protein-structure prediction-statistical potential and genetic algorithms
    • Sun S. J. Reduced representation model of protein-structure prediction-statistical potential and genetic algorithms. Protein Sci. 2:1993;762-785.
    • (1993) Protein Sci. , vol.2 , pp. 762-785
    • Sun, S.J.1
  • 26
    • 0028841399 scopus 로고
    • A simple protein-folding algorithm using a binary code and secondary structure constraints
    • Sun S. J., Thomas P. D., Dill K. A. A simple protein-folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:1995;769-778.
    • (1995) Protein Eng. , vol.8 , pp. 769-778
    • Sun, S.J.1    Thomas, P.D.2    Dill, K.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.