The SAAP force field. A simple approach to a new all‐atom protein force field by using single amino acid potential (SAAP) functions in various solvents*

Iwaoka, Michio; Tomoda, Shuji

doi:10.1002/jcc.10259

Cited by 19 publications

(35 citation statements)

References 59 publications

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“…The potential energy of the connected molecule was finally calculated as the sum of potential energies of the main-chain and side-chain units and the electrostatic and LJ potentials between the atoms belonging to the connected units, except for the interactions involving C a or C b atom. Conventional equations in the literature 22 were used for the calculation of electrostatic and LJ potentials.…”

Section: Side-chain Separation Approximationmentioning

confidence: 99%

“…(2)], which utilizes single amino acid potentials (SAAP) as the fundamental elements. 22 Contract/grant sponsor: The Ministry of Education, Culture, Sports, Science and Technology of Japan (Grants-in-Aid for Scientific Research (B); contract/grant number: 16350092 Contract/grant sponsor: The Tokai University Educational System General Research Organization (Protein project) *The SAAP simulation program is available from the corresponding author upon request.…”

Section: Introductionmentioning

confidence: 99%

“…In this article, we have developed whole sets of the SAAP force field parameters in vacuo, in ether, and in water by ab initio calculation for all 20 proteinogenic amino acids as the extension from a previous version of the SAAP force field, 22 which contained the parameters only for Gly and Ala. To obtain the SAAP parameters for the amino acids with a long side chain, a side-chain separation approximation (Fig. 2) was applied.…”

Section: Introductionmentioning

confidence: 99%

“…In this all-atom force field, called SAAP, 22 the total potential energy of a polypeptide molecule (E total ) is divided into SAAPs of the individual amino acid units (E SAAP ) and the interamino acid interactions (E inter ). The correlation term between these terms (E others ) should be included to attain the exact potential energy function, 23 but the E others term is currently ignored as a constant because the contribution to the total potential energy would be small compared with the other two terms [see eq.…”

Section: Introductionmentioning

confidence: 99%

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The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like beta-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units.

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Section: Side-chain Separation Approximationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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“…The Fourier series can express the torsion-energy surface E(φ, ψ) that was obtained by any method including quantum chemistry calculations. [6,15,16,17,18,19] Moreover, one can refine the existing backbone-torsion-energy term and control the secondary-structure-forming tendencies of the force fields. For example, α-helix is obtained for (φ,ψ) ≈ (−57…”

Section: Methodsmentioning

confidence: 99%

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

Sakae

Okamoto

2006

J. Phys. Soc. Jpn.

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We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase/decrease the α-helix-forming-tendencies by lowering/raising the torsion-energy surface in the α-helix region and likewise increase/decrease the β-sheet-forming tendencies by lowering/raising the surface in the β-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming-tendencies by performing folding simulations of α-helical and β-hairpin peptides.

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Optimizations of Protein Force Fields

Sakae¹,

Okamoto²

2018

Springer Series on Bio- And Neurosystems

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In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various methods for force-field parameter optimizations. Finally, some examples of our applications of these parameter optimization methods are given and they are compared with the results from the existing force-fields.

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The SAAP force field. A simple approach to a new all‐atom protein force field by using single amino acid potential (SAAP) functions in various solvents*

Cited by 19 publications

References 59 publications

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

Secondary-Structure Design of Proteins by a Backbone Torsion Energy

Optimizations of Protein Force Fields

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