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Volumn 57, Issue 4, 2004, Pages 792-798

All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method

Author keywords

Biomolecular structure prediction; Free energy forcefield; HIV accessory protein; Protein folding; Stochastic optimization

Indexed keywords

HELIX LOOP HELIX PROTEIN; HIV ACCESSORY PROTEIN; UNCLASSIFIED DRUG;

EID: 10344222927     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20290     Document Type: Article
Times cited : (32)

References (37)
  • 1
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 4
    • 0642285282 scopus 로고    scopus 로고
    • Reproducible protein folding with the stochastic tunneling method
    • Schug A, Herges T, Wenzel W. Reproducible protein folding with the stochastic tunneling method. Phys Rev Lett 2003;91:158102.
    • (2003) Phys Rev Lett , vol.91 , pp. 158102
    • Schug, A.1    Herges, T.2    Wenzel, W.3
  • 6
    • 0344304436 scopus 로고    scopus 로고
    • Atomically detailed folding simulation of the b domain of staphylococcal protein a from random structures
    • Vila JA, Ripoll DR, Scheraga HA. Atomically detailed folding simulation of the b domain of staphylococcal protein a from random structures. Proc Natl Acad Sci USA 2004;100:14812-14816.
    • (2004) Proc Natl Acad Sci USA , vol.100 , pp. 14812-14816
    • Vila, J.A.1    Ripoll, D.R.2    Scheraga, H.A.3
  • 7
    • 0042311829 scopus 로고    scopus 로고
    • Global optimization by energy landscape paving
    • Hansmann UHE. Global optimization by energy landscape paving. Phys Rev Lett 2002;88:068105.
    • (2002) Phys Rev Lett , vol.88 , pp. 068105
    • Hansmann, U.H.E.1
  • 8
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews J. Drug discovery: a historical perspective. Science 2000;287:1960-1964.
    • (2000) Science , vol.287 , pp. 1960-1964
    • Drews, J.1
  • 9
    • 0037424459 scopus 로고    scopus 로고
    • Application of the stochastic tunneling method to high throughput screening
    • Merlitz H, Burghardt B, Wenzel W. Application of the stochastic tunneling method to high throughput screening. Chem Phys Lett 2003;370:68-73.
    • (2003) Chem Phys Lett , vol.370 , pp. 68-73
    • Merlitz, H.1    Burghardt, B.2    Wenzel, W.3
  • 12
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 13
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein folding dynamics
    • Snow CD, Nguyen H, Panda VS, Gruebele M. Absolute comparison of simulated and experimental protein folding dynamics. Nature 2002;420:102-106.
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, H.2    Panda, V.S.3    Gruebele, M.4
  • 14
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C, Strockbine B, Roitberg A. All-atom structure prediction and folding simulations of a stable protein. J Am Chem Soc 2002;124:11258-11259.
    • (2002) J Am Chem Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.3
  • 15
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 16
    • 0023430366 scopus 로고
    • Monte Carlo minimization approach to the multiple minima problem in protein folding
    • Li Z, Scheraga HA. Monte Carlo minimization approach to the multiple minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 17
    • 0037133165 scopus 로고    scopus 로고
    • A method for optimising potential energy functions by a hierarchical design of the potential energy landscape
    • Liwo A, Arlukowicz P, Czaplewski C, Oldizeij S, Pillardy J, Scheraga HA. A method for optimising potential energy functions by a hierarchical design of the potential energy landscape. Proc Natl Acad Sci USA 2002;99:1937-1942.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 1937-1942
    • Liwo, A.1    Arlukowicz, P.2    Czaplewski, C.3    Oldizeij, S.4    Pillardy, J.5    Scheraga, H.A.6
  • 18
    • 10344236244 scopus 로고    scopus 로고
    • Development of an all-atom forcefield for tertiary structure prediction of helical proteins
    • In press
    • Herges T, Wenzel W. Development of an all-atom forcefield for tertiary structure prediction of helical proteins. Biophysical Journal. In press.
    • Biophysical Journal
    • Herges, T.1    Wenzel, W.2
  • 19
    • 0034700249 scopus 로고    scopus 로고
    • Biochemical and structural analysis of the interaction between the uba(2) domain of the dna repair protein hhr23a and hiv-1 vpr
    • Withers-Ward ES, Mueller TD, Chen IS, Feigon J. Biochemical and structural analysis of the interaction between the uba(2) domain of the dna repair protein hhr23a and hiv-1 vpr. Biochemistry 2000;39:14103-14112.
    • (2000) Biochemistry , vol.39 , pp. 14103-14112
    • Withers-Ward, E.S.1    Mueller, T.D.2    Chen, I.S.3    Feigon, J.4
  • 20
    • 0036308140 scopus 로고    scopus 로고
    • Stochastic optimisation methods for biomolecular structure prediction
    • Herges T, Merlitz H, Wenzel W. Stochastic optimisation methods for biomolecular structure prediction. J Assoc Lab Autom 2002;7:98-104.
    • (2002) J Assoc Lab Autom , vol.7 , pp. 98-104
    • Herges, T.1    Merlitz, H.2    Wenzel, W.3
  • 21
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformation searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov M. Biased probability Monte Carlo conformation searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
    • (1994) J Mol Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 22
    • 4544246504 scopus 로고    scopus 로고
    • Low energy conformations of a three helix peptide in an all-atom biomolecular forcefield
    • Herges T, Schug A, Burghardt B, Wenzel W. Low energy conformations of a three helix peptide in an all-atom biomolecular forcefield. Int J Quantum Chem 2004;99:854-863.
    • (2004) Int J Quantum Chem , vol.99 , pp. 854-863
    • Herges, T.1    Schug, A.2    Burghardt, B.3    Wenzel, W.4
  • 23
    • 0028960071 scopus 로고
    • Role of electrostatic screening in determining protein main chain conformational preferences
    • Avbelj F, Moult J. Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 1995;34:755-764.
    • (1995) Biochemistry , vol.34 , pp. 755-764
    • Avbelj, F.1    Moult, J.2
  • 24
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 25
    • 0026076664 scopus 로고
    • Extracting hydrophobic free energies from experimental data:relationship to protein folding and theoretical models
    • Sharp KA, Nicholls A, Friedman R, Honig B. Extracting hydrophobic free energies from experimental data:relationship to protein folding and theoretical models. Biochemistry 1991;30:9686-9697.
    • (1991) Biochemistry , vol.30 , pp. 9686-9697
    • Sharp, K.A.1    Nicholls, A.2    Friedman, R.3    Honig, B.4
  • 26
    • 0242618215 scopus 로고    scopus 로고
    • Stochastic optimization methods for structure prediction of biomolecular nanoscale systems
    • Herges T, Schug A, Merlitz H, Wenzel W. Stochastic optimization methods for structure prediction of biomolecular nanoscale systems. Nanotechnology 2003;14:1161-1167.
    • (2003) Nanotechnology , vol.14 , pp. 1161-1167
    • Herges, T.1    Schug, A.2    Merlitz, H.3    Wenzel, W.4
  • 29
    • 0142013225 scopus 로고    scopus 로고
    • Numerical comparison of three recently proposed algorithms in the protein folding problem
    • Hansmann UHE, Okamoto Y. Numerical comparison of three recently proposed algorithms in the protein folding problem. J Comput Chem 1997;18:920-933.
    • (1997) J Comput Chem , vol.18 , pp. 920-933
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 31
    • 0042171838 scopus 로고    scopus 로고
    • Parallel tempering simulations of HP-36
    • Lin CY, Hu CK, Hansmann UH. Parallel tempering simulations of HP-36. Proteins 2003;53:436-445.
    • (2003) Proteins , vol.53 , pp. 436-445
    • Lin, C.Y.1    Hu, C.K.2    Hansmann, U.H.3
  • 32
    • 0001616080 scopus 로고    scopus 로고
    • Ab initio replica-exchange Monte Carlo method for cluster studies
    • Sugita Y, Okamoto Y. Ab initio replica-exchange Monte Carlo method for cluster studies. Chem Phys Lett 1999;314:141-151.
    • (1999) Chem Phys Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 34
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein a
    • Garcia AE, Onuchic N. Folding a protein in a computer: an atomic description of the folding/unfolding of protein a. Proc Natl Acad Sci USA 2003;100:13898-13903.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13898-13903
    • Garcia, A.E.1    Onuchic, N.2
  • 35
    • 1442287309 scopus 로고    scopus 로고
    • Comparisons of force fields for proteins by generalized-ensemble simulations
    • Yoda T, Sugita Y, Okamoto Y. Comparisons of force fields for proteins by generalized-ensemble simulations. Chem Phys Lett 2004;386:460-467.
    • (2004) Chem Phys Lett , vol.386 , pp. 460-467
    • Yoda, T.1    Sugita, Y.2    Okamoto, Y.3
  • 36
    • 21144456638 scopus 로고    scopus 로고
    • Protein structure prediction with stochastic optimization methods: Folding and misfolding the villin headpiece
    • Herges T, Schug A, Wenzel W. Protein structure prediction with stochastic optimization methods: folding and misfolding the villin headpiece. Lecture Notes in Computational Science. 2004;3045:454-464.
    • (2004) Lecture Notes in Computational Science , vol.3045 , pp. 454-464
    • Herges, T.1    Schug, A.2    Wenzel, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.