메뉴 건너뛰기




Volumn 4414 LNBI, Issue , 2007, Pages 381-394

Stochastic protein folding simulation in the d-dimensional HP-model

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; MARKOV PROCESSES; MATHEMATICAL MODELS;

EID: 34548086584     PISSN: 03029743     EISSN: 16113349     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (9)

References (53)
  • 1
    • 0043043359 scopus 로고    scopus 로고
    • On the complexity of string folding
    • Paterson, M., Przytycka, T.: On the complexity of string folding. Discrete Appl. Math. 71 (1996) 217-230.
    • (1996) Discrete Appl. Math , vol.71 , pp. 217-230
    • Paterson, M.1    Przytycka, T.2
  • 2
    • 0031897962 scopus 로고    scopus 로고
    • Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete
    • Berger, B., Leighton, T.: Protein folding in the hydrophobic-hydrophilic (HP) model is NP-complete. J. Comput. Biol. 5 (1998) 27-40.
    • (1998) J. Comput. Biol , vol.5 , pp. 27-40
    • Berger, B.1    Leighton, T.2
  • 3
    • 0032946512 scopus 로고    scopus 로고
    • Spatial codes and the hardness of string folding problems
    • Nayak, A., Sinclair, A, Zwick, U.: Spatial codes and the hardness of string folding problems. J. Comput. Biol. 6 (1999) 13-36.
    • (1999) J. Comput. Biol , vol.6 , pp. 13-36
    • Nayak, A.1    Sinclair, A.2    Zwick, U.3
  • 4
    • 0028929556 scopus 로고    scopus 로고
    • Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M.: D.P. Yee, P.D. Thomas, H.S. Chan, Principles of protein folding - A perspective from simple exact models. Protein Sci. 4 (1995) 561-602.
    • Dill, K.A., Bromberg, S., Yue, K., Fiebig, K.M.: D.P. Yee, P.D. Thomas, H.S. Chan, Principles of protein folding - A perspective from simple exact models. Protein Sci. 4 (1995) 561-602.
  • 6
    • 4544326903 scopus 로고    scopus 로고
    • Opportunities for combinatorial optimization in computational biology
    • Greenberg, H.J., Hart, W.E., Lancia, G.: Opportunities for combinatorial optimization in computational biology. INFORMS J. Comput. 16 (2004) 211-231.
    • (2004) INFORMS J. Comput , vol.16 , pp. 211-231
    • Greenberg, H.J.1    Hart, W.E.2    Lancia, G.3
  • 7
    • 33244480262 scopus 로고    scopus 로고
    • Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins
    • Schiemann, R., Bachmann, M., Janke, W.: Exact sequence analysis for three-dimensional hydrophobic-polar lattice proteins. J. Chem. Phys. 122 (2005) 114705.
    • (2005) J. Chem. Phys , vol.122 , pp. 114705
    • Schiemann, R.1    Bachmann, M.2    Janke, W.3
  • 8
    • 35048887620 scopus 로고    scopus 로고
    • O(n1-1/d·log n) time algorithm for d-dimensional protein folding in the HP-model
    • st International Colloquium on Automata, Languages and Programming, pp, Springer-Verlag, Heidelberg
    • st International Colloquium on Automata, Languages and Programming, pp. 630-644. LNCS 3142, Springer-Verlag, Heidelberg, 2004.
    • (2004) LNCS , vol.3142 , pp. 630-644
    • Fu, B.1    Wang, W.2
  • 9
    • 0030737872 scopus 로고    scopus 로고
    • Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal
    • Hart, W.E., Istrail, S.: Lattice and off-lattice side chain models of protein folding: Linear time structure prediction better than 86% of optimal. J. Comput. Biol. 4 (1997) 241-260
    • (1997) J. Comput. Biol , vol.4 , pp. 241-260
    • Hart, W.E.1    Istrail, S.2
  • 10
    • 0037375005 scopus 로고    scopus 로고
    • Approximate protein folding in the HP side chain model on extended cubic lattices
    • Heun, V. Approximate protein folding in the HP side chain model on extended cubic lattices. Discrete Appl. Math. 127 (2003) 163-177.
    • (2003) Discrete Appl. Math , vol.127 , pp. 163-177
    • Heun, V.1
  • 11
    • 0030623529 scopus 로고    scopus 로고
    • Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold
    • Finkelstein, A.V., Badretdinov, A.Y.: Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. Fold. Des. 2 (1997) 115-121.
    • (1997) Fold. Des , vol.2 , pp. 115-121
    • Finkelstein, A.V.1    Badretdinov, A.Y.2
  • 13
    • 0037402639 scopus 로고    scopus 로고
    • Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics
    • Galzitskaya, O.V., Garbuzynskiy, S.O., Ivankov, D.N., Finkelstein, A.V.: Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins 51 (2003) 162-166.
    • (2003) Proteins , vol.51 , pp. 162-166
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Ivankov, D.N.3    Finkelstein, A.V.4
  • 14
    • 1342281633 scopus 로고    scopus 로고
    • The protein folding 'speed limit'. Curr. Opin. Struc. Biol
    • 76-88
    • Kubelka, J., Hofrichter, J., Eaton, W.A.: The protein folding 'speed limit'. Curr. Opin. Struc. Biol. 14 (2004) 76-88.
    • (2004) , vol.14
    • Kubelka, J.1    Hofrichter, J.2    Eaton, W.A.3
  • 15
    • 4143101125 scopus 로고    scopus 로고
    • Guiding the search for a protein's maximum rate of folding
    • Zhu, Y., Fu, X., Wang, T., Tamura, A., Takada, S., Saven, J.G.: Guiding the search for a protein's maximum rate of folding. Chem. Phys. 307 (2004) 99-109.
    • (2004) Chem. Phys , vol.307 , pp. 99-109
    • Zhu, Y.1    Fu, X.2    Wang, T.3    Tamura, A.4    Takada, S.5    Saven, J.G.6
  • 17
    • 0347123330 scopus 로고    scopus 로고
    • Thermal denaturation and folding rates of single domain proteins: Size matters
    • Li, M.S., Klimov, D.K., Thirumalai, D.: Thermal denaturation and folding rates of single domain proteins: size matters. Polymer 45 (2004) 573-579.
    • (2004) Polymer , vol.45 , pp. 573-579
    • Li, M.S.1    Klimov, D.K.2    Thirumalai, D.3
  • 18
    • 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
  • 19
    • 0001628920 scopus 로고
    • Conformational analysis of flexible molecules: Location of the global minimum energy conformation by the simulated annealing method
    • Wilson, S.R., Cui, W., Moskowitz, J.W., Schmidt, K.E.: Conformational analysis of flexible molecules: Location of the global minimum energy conformation by the simulated annealing method. Tetrahedron Lett. 29 (1988) 4373-4376.
    • (1988) Tetrahedron Lett , vol.29 , pp. 4373-4376
    • Wilson, S.R.1    Cui, W.2    Moskowitz, J.W.3    Schmidt, K.E.4
  • 20
    • 0024789103 scopus 로고
    • A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method
    • Kawai, H., Kikuchi, T., Okamoto, Y.: A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method, Protein Eng. 3 (1989) 85-94.
    • (1989) Protein Eng , vol.3 , pp. 85-94
    • Kawai, H.1    Kikuchi, T.2    Okamoto, Y.3
  • 22
    • 0021819411 scopus 로고
    • A thermodynamical approach to the travelling salesman problem: An efficient simulation algorithm
    • Černý, V.: A thermodynamical approach to the travelling salesman problem: an efficient simulation algorithm. J. Optimiz. Theory App. 45 (1985) 41-51.
    • (1985) J. Optimiz. Theory App , vol.45 , pp. 41-51
    • Černý, V.1
  • 23
    • 0022105875 scopus 로고
    • Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin
    • Paine, G.H., Scheraga, H.A.: Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin. Biopolymers 24 (1985) 1391-1436.
    • (1985) Biopolymers , vol.24 , pp. 1391-1436
    • Paine, G.H.1    Scheraga, H.A.2
  • 25
    • 0000800852 scopus 로고    scopus 로고
    • Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering
    • Hansmann, U.H.E., Okamoto, Y.: Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering. Phys. Rev. E 54 (1996) 5863-5865.
    • (1996) Phys. Rev. E , vol.54 , pp. 5863-5865
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 26
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger, R., Moult, J.: Genetic algorithms for protein folding simulations. J. Mol. Biol. 231 (1993) 75-81.
    • (1993) J. Mol. Biol , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 27
    • 0029786785 scopus 로고    scopus 로고
    • Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator
    • Rabow, A.A., Scheraga, H.A.: Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator. Protein Sci 5 (1996) 1800-1815.
    • (1996) Protein Sci , vol.5 , pp. 1800-1815
    • Rabow, A.A.1    Scheraga, H.A.2
  • 28
    • 0346950252 scopus 로고    scopus 로고
    • Protein conformation of a lattice model using tabu search
    • Pardalos, P.M., Liu, X., Xue, G.: Protein conformation of a lattice model using tabu search. J. Global Optim. 11 (1997) 55-68.
    • (1997) J. Global Optim , vol.11 , pp. 55-68
    • Pardalos, P.M.1    Liu, X.2    Xue, G.3
  • 29
    • 0036681613 scopus 로고    scopus 로고
    • Generalized ensemble techniques and protein folding simulations
    • Hansmann, U.H.E.: Generalized ensemble techniques and protein folding simulations, Comput. Phys. Commun. 147 (2002) 604-607.
    • (2002) Comput. Phys. Commun , vol.147 , pp. 604-607
    • Hansmann, U.H.E.1
  • 30
    • 31544448267 scopus 로고    scopus 로고
    • An enhanced version of SMMP-open-source software package for simulation of proteins
    • Eisenmenger, F., Hansmann, U.H.E., Hayryan, S., Hu, C.K.: An enhanced version of SMMP-open-source software package for simulation of proteins. Comput. Phys. Commun. 174 (2006) 422-429.
    • (2006) Comput. Phys. Commun , vol.174 , pp. 422-429
    • Eisenmenger, F.1    Hansmann, U.H.E.2    Hayryan, S.3    Hu, C.K.4
  • 31
    • 0035250027 scopus 로고    scopus 로고
    • Simulation of protein folding by reaction path annealing
    • Eastman, P., Grønbech-Jensen, N., Doniach, S.: Simulation of protein folding by reaction path annealing. J. Chem. Phys. 114 (2001) 3823-3841.
    • (2001) J. Chem. Phys , vol.114 , pp. 3823-3841
    • Eastman, P.1    Grønbech-Jensen, N.2    Doniach, S.3
  • 32
    • 0037445044 scopus 로고    scopus 로고
    • A new class of hybrid global optimization algorithms for peptide structure prediction: Integrated hybrids
    • Klepeis, J.L., Pieja, M.J., Floudas, C.A.: A new class of hybrid global optimization algorithms for peptide structure prediction: integrated hybrids. Comput. Phys. Commun. 151 (2003) 121-140.
    • (2003) Comput. Phys. Commun , vol.151 , pp. 121-140
    • Klepeis, J.L.1    Pieja, M.J.2    Floudas, C.A.3
  • 34
    • 0024012393 scopus 로고
    • Cooling schedules for optimal annealing
    • Hajek, B.: Cooling schedules for optimal annealing. Mathem. Oper. Res. 13 (1988) 311-329.
    • (1988) Mathem. Oper. Res , vol.13 , pp. 311-329
    • Hajek, B.1
  • 35
    • 0000305088 scopus 로고
    • A limit theorem for a class of inhomogeneous Markov processes
    • Chiang, T.S., Chow, Y.Y.: A limit theorem for a class of inhomogeneous Markov processes. Ann. Probab. 17 (1989) 1483-1502.
    • (1989) Ann. Probab , vol.17 , pp. 1483-1502
    • Chiang, T.S.1    Chow, Y.Y.2
  • 36
    • 0001621836 scopus 로고
    • Rough large deviation estimates for simulated annealing: Applications to exponential schedules
    • Catoni, O.: Rough large deviation estimates for simulated annealing: applications to exponential schedules. Ann. Probab. 20 (1992) 1109-1146.
    • (1992) Ann. Probab , vol.20 , pp. 1109-1146
    • Catoni, O.1
  • 37
    • 0030295649 scopus 로고    scopus 로고
    • Simulated annealing with time dependent energy function via Sobolev inequalities
    • Löwe, M.: Simulated annealing with time dependent energy function via Sobolev inequalities. Stoch. Proc. Appl. 63 (1996) 221-233.
    • (1996) Stoch. Proc. Appl , vol.63 , pp. 221-233
    • Löwe, M.1
  • 38
    • 0035658660 scopus 로고    scopus 로고
    • Convergence and first hitting time of simulated annealing algorithms for continuous global optimization
    • Locatelli, M.: Convergence and first hitting time of simulated annealing algorithms for continuous global optimization. Math. Meth. Oper. Res. 54 (2001) 171-199.
    • (2001) Math. Meth. Oper. Res , vol.54 , pp. 171-199
    • Locatelli, M.1
  • 39
    • 84867959651 scopus 로고    scopus 로고
    • On the convergence of generalized hill climbing algorithms
    • Johnson, A.W., Jacobson, S.H.: On the convergence of generalized hill climbing algorithms. Discrete Appl. Math. 119 (2002) 37-57.
    • (2002) Discrete Appl. Math , vol.119 , pp. 37-57
    • Johnson, A.W.1    Jacobson, S.H.2
  • 40
    • 30344481937 scopus 로고    scopus 로고
    • Sufficient and necessary condition for the convergence of stochastic approximation algorithms
    • Chen, N., Liu, W., Feng, J.: Sufficient and necessary condition for the convergence of stochastic approximation algorithms. Stat. Probabil. Lett. 76 (2006) 203-210.
    • (2006) Stat. Probabil. Lett , vol.76 , pp. 203-210
    • Chen, N.1    Liu, W.2    Feng, J.3
  • 41
    • 0036494672 scopus 로고    scopus 로고
    • Combinatorial landscapes
    • Reidys, C.M., Stadler, P.F.: Combinatorial landscapes. SIAM Rev. 44 (2002) 3-54.
    • (2002) SIAM Rev , vol.44 , pp. 3-54
    • Reidys, C.M.1    Stadler, P.F.2
  • 42
    • 33748304086 scopus 로고    scopus 로고
    • A stopping criterion for logarithmic simulated annealing
    • Albrecht, A.A.: A stopping criterion for logarithmic simulated annealing. Computing 78 (2006) 55-79.
    • (2006) Computing , vol.78 , pp. 55-79
    • Albrecht, A.A.1
  • 43
    • 10644265361 scopus 로고    scopus 로고
    • A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC)
    • Backofen, R.: A polynomial time upper bound for the number of contacts in the HP-model on the face-centered-cubic lattice (FCC). J. Discrete Algorithms 2 (2004) 161-206.
    • (2004) J. Discrete Algorithms , vol.2 , pp. 161-206
    • Backofen, R.1
  • 46
    • 24144487043 scopus 로고    scopus 로고
    • Application of tabu search strategy for finding low energy structure of protein
    • Blazewicz, J., Lukasiak, P., Milostan, M.: Application of tabu search strategy for finding low energy structure of protein. Artif. Intell. Med. 35 (2005) 135-145.
    • (2005) Artif. Intell. Med , vol.35 , pp. 135-145
    • Blazewicz, J.1    Lukasiak, P.2    Milostan, M.3
  • 47
    • 0029909775 scopus 로고    scopus 로고
    • A fast conformational search strategy for finding low energy structures of model proteins
    • Beutler, T.C., Dill, K.A.: A fast conformational search strategy for finding low energy structures of model proteins. Protein Sci. 5 (1996) 2037-2043.
    • (1996) Protein Sci , vol.5 , pp. 2037-2043
    • Beutler, T.C.1    Dill, K.A.2
  • 48
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen, C.B.: Principles that govern the folding of protein chains. Science 181 (1973) 223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 49
    • 0031236591 scopus 로고    scopus 로고
    • Molecular modeling of proteins and mathematical prediction of protein structure
    • Neumaier, A.: Molecular modeling of proteins and mathematical prediction of protein structure. SIAM Rev. 39 (1997) 407-460.
    • (1997) SIAM Rev , vol.39 , pp. 407-460
    • Neumaier, A.1
  • 51
    • 0035327183 scopus 로고    scopus 로고
    • Evaluating protein structure-prediction schemes using energy landscape theory
    • Eastwood, M.P., Hardin, C., Luthey-Schulten, Z., Wolynes, P.G.: Evaluating protein structure-prediction schemes using energy landscape theory. IBM J. Res. Develop. 45 (2001) 475-497.
    • (2001) IBM J. Res. Develop , vol.45 , pp. 475-497
    • Eastwood, M.P.1    Hardin, C.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 52
    • 0042797442 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge
    • Wales, D.: Energy landscapes. Cambridge University Press, Cambridge, 2003.
    • (2003) Energy landscapes
    • Wales, D.1
  • 53
    • 21644454399 scopus 로고    scopus 로고
    • Finding pathways between distant local minima
    • Carr, J.M., Trygubenko, S.A., Wales, D.J.: Finding pathways between distant local minima. J. Chem. Phys. 122 (2005) 234903.
    • (2005) J. Chem. Phys , vol.122 , pp. 234903
    • Carr, J.M.1    Trygubenko, S.A.2    Wales, D.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.