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Volumn 46, Issue 1, 2002, Pages 128-146

Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ALANYLALANINE; BARNASE; CRAMBIN; PEPTIDE; UNCLASSIFIED DRUG; VILLIN; WATER;

EID: 0036137805     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10020     Document Type: Article
Times cited : (63)

References (107)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 15
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    • (2000) J Comput Chem , vol.21 , pp. 105-120
    • MacKerell, J.1    Banavali, N.2
  • 19
    • 0032579189 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
    • (1998) J Mol Biol , vol.275 , pp. 677-694
    • Li, A.1    Daggett, V.2
  • 23
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 24
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • (2000) Proteins , vol.39 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 30
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized born solvation model
    • (2000) J Am Chem Soc , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 31
    • 11644251375 scopus 로고    scopus 로고
    • Comparison of a GB solvation model with explicit solvent simulations: Potential of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane
    • (1997) J Phys Chem B , vol.102 , pp. 3636-3640
    • Scarsi, M.1    Apostolakis, J.2    Caflisch, A.3
  • 39
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • (1999) Biophys Chem , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 40
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 53
    • 0034237485 scopus 로고    scopus 로고
    • Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data
    • (2000) Proteins , vol.40 , pp. 145-153
    • Stocker, U.1    Van Gunsteren, W.F.2
  • 64
    • 0032744232 scopus 로고    scopus 로고
    • Protein folding: From the levinthal paradox to structure prediction
    • (1999) J Mol Biol , vol.293 , pp. 283-293
    • Honig, B.1
  • 68
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 69
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
    • (1994) Proteins , vol.20 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard III, W.A.4
  • 75
    • 0032620117 scopus 로고    scopus 로고
    • Improved ab initio predictions with a simplified, flexible geometry model
    • (1999) Proteins , Issue.3 SUPPL. , pp. 186-193
    • Osguthorpe, D.J.1
  • 86
    • 0026076664 scopus 로고
    • Extracting hydrophobic free energies from experimental data: Relationship to protein folding and theoretical models
    • published erratum appears in Biochemistry 1993 May 25;32(20):5490
    • (1991) Biochemistry , vol.30 , pp. 9686-9697
    • Sharp, K.A.1    Nicholls, A.2    Friedman, R.3    Honig, B.4
  • 89
    • 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
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 93
    • 0022423920 scopus 로고
    • Theory for the folding and stability of globular proteins
    • (1985) Biochemistry , vol.24 , pp. 1501-1509
    • Dill, K.A.1
  • 102
    • 0032606104 scopus 로고    scopus 로고
    • RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
    • (1999) Proteins , vol.37 , Issue.S3 , pp. 15-21
    • Hubbard, T.J.1
  • 106
    • 0033516512 scopus 로고    scopus 로고
    • Analysis methods for comparison of multiple molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles
    • (1999) J Mol Biol , vol.290 , pp. 283-304
    • Kazmirski, S.L.1    Li, A.2    Daggett, V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.