J.-E. Shea, Y.D. Nochomovitz, Z. Guo and C.L Brooks, III, Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist fi-barrel model, J. Chem. Phys, 109 (1998), pp. 2895--2903  Home/Search Document Not in Database Summary Related Articles Check |
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A Test Set for Molecular Dynamics Algorithms - Barth, Leimkuhler, Reich (2002) (Correct)
....as in the Grubmuller model with bonds replaced by algebraic constraints, while the nonbonded interactions are modeled by the LJ potential with parameters for interaction between specific pairs chosen to reflect properties of individual residues in the amino acid sequence. Details can be found in [101]. 4 Conclusions In this paper, we have presented a number of small model systems for use in testing and comparing molecular dynamics algorithms. Beginning with an atomic fluid, we have sequentially treated systems of increasing molecular complexity which possess important features of the ....
J.-E. Shea, Y.D. Nochomovitz, Z. Guo and C.L Brooks, III, Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist fi-barrel model, J. Chem. Phys, 109 (1998), pp. 2895--2903
Three-helix-bundle Protein in a Ramachandran Model - Irbäck, Sjunnesson, Wallin (2000) (Correct)
....of the hydrogen bond and hydrophobicity terms on the basis of the resulting overall thermodynamic behavior of the three helix sequence. For this purpose, we performed a set of trial runs for fixed values of the other parameters. An alternative would have been to use the method of Shea et al. [33]. The result of our empirical determination of ffl hb and ffl AA does not seem unreasonable; at the folding temperature of the three helix sequence (see below) we get ffl hb =kT 4:3 and ffl AA =kT 3:4. In this model, we study the three sequences shown in Table 3, which contain 16, 35 y The ....
....this behavior, although its hydrogen bonds are context independent. Let us finally stress that we find a first order like folding transition without using the Go approximation. Evidence for first order like folding transitions has been found for proteins with similar lengths in some C ff models [5, 14, 17, 33], but these studies use this approximation. Acknowledgements This work was in part supported by the Swedish Foundation for Strategic Research. 12 ....
Shea, J.-E., Nochomovitz, Y.D., Guo, Z. & Brooks, C.L., III (1998) "Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist fi-barrel Model", J. Chem. Phys. 109, 2895--2903.
Three-helix-bundle Protein in a Ramachandran Model - Irbäck, Sjunnesson, Wallin (2000) (Correct)
....strengths of the hydrogen bond and hydrophobicity terms based on the resulting overall thermodynamic behavior of the three helix sequence. For this purpose we performed a set of trial runs, for fixed values of the other parameters. An alternative would have been to use the method of Shea et al. [33]. The result of our empirical determination of ffl hb and ffl AA does not seem unreasonable; at the folding temperature of the three helix sequence (see below) we get ffl hb =kT 4:3 and ffl AA =kT 3:4. In this model we study the three sequences shown in Table 3, which contain 16, 35 y The ....
....effect can be reproduced using pairwise interactions only. Let us finally stress the fact that we find a first order like folding transition without using the Go approximation. Evidence for first order like folding transitions has been found for proteins with similar lengths in some C ff models [5, 14,17,33] and also in a model at atomic resolution [37] but these studies use this approximation. Acknowledgements This work was in part supported by the Swedish Foundation for Strategic Research. 12 ....
Shea, J.-E., Nochomovitz, Y.D., Guo, Z. & Brooks, C.L., III (1998) "Exploring the Space of Protein Folding Hamiltonians: The Balance of Forces in a Minimalist fi-barrel Model", J. Chem. Phys. 109, 2895--2903.
Folding of a Small Helical Protein Using Hydrogen Bonds.. - Favrin, Irbäck, Wallin (2002) (Correct)
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Shea J-E, Nochomovitz YD, Guo Z, Brooks CL III. Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist -barrel model. J. Chem. Phys. 1998 ; 109 : 2895-2903.
Redesigning the Hydrophobic Core of a Model beta-sheet.. - Sorenson, Head-Gordon (1999) (Correct)
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Shea J E, Nochomovitz YD, Guo Z, Brooks CL. Exploring the space of protein folding hamiltonians: The balance of forces in a minimalist fi-barrel model. J. Chem. Phys. 1998;109:2895--2903.
Matching Simulation and Experiment: A New Simplified Model for .. - Sorenson, al. (1999) (Correct)
No context found.
Shea J E, Nochomovitz YD, Guo Z, Brooks CL. Exploring the space of protein folding hamiltonians: The balance of forces in a minimalist fi-barrel model. J. Chem. Phys. 1998;109:2895--2903.
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