Assessing the One-Bond C α -H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches
In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the be...
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| Veröffentlicht in: | The journal of physical chemistry. B Jg. 124; H. 5; S. 735 |
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06.02.2020
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| Abstract | In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC)
in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the
SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed
SSCC values. Further analysis leads us to the understanding that the model chosen for the DFT computations is inappropriate and that more complex models will require a higher, if not prohibitively, computational cost. Finally, we show that the Karplus-like equation and Gaussian Process regression provide faster and more accurate results than DFT-based calculations. |
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| AbstractList | In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1JCαH in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the 1JCαH SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed 1JCαH SSCC values. Further analysis leads us to the understanding that the model chosen for the DFT computations is inappropriate and that more complex models will require a higher, if not prohibitively, computational cost. Finally, we show that the Karplus-like equation and Gaussian Process regression provide faster and more accurate results than DFT-based calculations.In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1JCαH in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the 1JCαH SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed 1JCαH SSCC values. Further analysis leads us to the understanding that the model chosen for the DFT computations is inappropriate and that more complex models will require a higher, if not prohibitively, computational cost. Finally, we show that the Karplus-like equation and Gaussian Process regression provide faster and more accurate results than DFT-based calculations. In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed SSCC values. Further analysis leads us to the understanding that the model chosen for the DFT computations is inappropriate and that more complex models will require a higher, if not prohibitively, computational cost. Finally, we show that the Karplus-like equation and Gaussian Process regression provide faster and more accurate results than DFT-based calculations. |
| Author | Scheraga, Harold A Arroyuelo, Agustina Martin, Osvaldo A Vila, Jorge A |
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| Snippet | In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC)
in proteins: density... In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1JCαH in proteins: density... |
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| SubjectTerms | Carbon - chemistry Density Functional Theory Hydrogen - chemistry Models, Chemical Nuclear Magnetic Resonance, Biomolecular - methods Proteins - chemistry Regression Analysis |
| Title | Assessing the One-Bond C α -H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches |
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