wanyu/IteraTeR_full_sent huggingface dataset:
Original: Molecular dynamics (MD) simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase protein and compared with quantum mechanical (QM) methods rooted on density functional theory (DFT).
Revised: Molecular dynamics (MD) simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) Aurora-A kinase protein and compared with quantum mechanical (QM) methods rooted on density functional theory (DFT).
Edit intent: clarity
Original: Molecular dynamics (MD) simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase protein and compared with quantum mechanical (QM) methods rooted on density functional theory (DFT). MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised: Molecular dynamics (MD) simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase activation loop in a very short time and with good quality of the sampling. The MD simulation provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: meaning-changed
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information on the interactions between MTSL and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: clarity
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and protein residues, and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: meaning-changed
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL that were validated using a multifrequency electron paramagnetic resonance (EPR) approach. The latter relayed on the frequency dependence of the resolution of the fast and slow motions of the spin probe and was used to distinguish the fast internal motion of the spin label from the slow protein tumbling. Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: meaning-changed
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: clarity
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from quantum mechanical (QM) methods, but more interactions within the dynamics of the system revealed more interactions than those observed from QMmethods .
Edit intent: clarity
Original:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and  on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QMmethods .
Revised:  MD provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL . Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system were revealed than from QM .
Edit intent: clarity
Original:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space .
Revised:  A strong correlation between the tumbling of the protein and the transitions of the X4 dihedral angle of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space .
Edit intent: clarity
Original:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space .
Revised:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space .
Edit intent: fluency
Original:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space .
Revised:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect on the distribution of the nitroxide (NO) group in the space .
Edit intent: clarity
Original:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in the space . Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein were seen to be in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system.
Revised:  A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL , was observed with a consequent effect also the distribution of the nitroxide (NO) group in space and time. The theoretical EPR spectra were calculated using selected configurations of MTSL probing different micro-environments of the protein were seen to be in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system.
Edit intent: clarity
Original:  Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein were seen to be in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system.
Revised:  Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein characterized by different polarity. The comparison between the theoretical and experimental 9 GHz and 94 GHz EPR spectra revealed that some fits were in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system.
Edit intent: meaning-changed
Original:  Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein were seen to be in good agreement with the experimental EPR spectrum , indicating a predominance of some conformational states of the full spin-labelled system.
Revised:  Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions between the MTSL and residues of the protein were seen to be in good agreement with the experimental EPR spectra , indicating a predominance of some conformational states of the full spin-labelled system.
Edit intent: fluency
Original: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost and good quality of the sampling the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase.
Revised: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase.
Edit intent: coherence
Original: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost and good quality of the sampling the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase.
Revised: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost and good quality of the sampling the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of Aurora-A kinase.
Edit intent: fluency
Original:  MD provided a wealth of information about the timescale of the different motional contributions to the overall dynamics of the spin label . These data were validated by multi-frequency continuous-wave electron paramagnetic resonance (EPR) measurements, that relying on the frequency dependence of the fast and slow motions of the spin probe were used to distinguish the fast internal motion of the spin label from slow protein tumbling.
Revised:  MD provided a wealth of information about the timescale of the different motional contributions to the overall dynamics of the spin label in space was found due to the large exposure of the activation loop to the solvent water. A hydrodynamic approach was employed to determine the rotational protein tumbling, while the internal motion of the spin label from slow protein tumbling.
Edit intent: meaning-changed
Original:  These data were validated by multi-frequency continuous-wave electron paramagnetic resonance (EPR) measurements, that relying on the frequency dependence of the fast and slow motions of the spin probe were used to distinguish the fast internal motion of the spin label from slow protein tumbling. It was found that the activation loop oscillated between two conformational states separated by 7 Angstrom and the average structures obtained from the MD trajectories showed the MTSL exposed to the solvent and probing the C-lobe of the protein .
Revised:  These data were validated by multi-frequency continuous-wave electron paramagnetic resonance (EPR) measurements, that relying on the frequency dependence of the fast and slow motions of the spin probe were used to distinguish the fast internal motion of the spin probe was determined from 94 GHz measurements that reflect the fast motions .
Edit intent: meaning-changed
Original:  The theoretical 9 and 94 GHz EPR spectra were calculated using configurations representing the interactions between MTSL and water and the tyrosine residue 208 in the C-lobe ;
Revised:  The theoretical 9 and 94 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe ;
Edit intent: fluency
Original:  The theoretical 9 and 94 GHz EPR spectra were calculated using configurations representing the interactions between MTSL and water and the tyrosine residue 208 in the C-lobe ;
Revised:  The theoretical 9 and 94 GHz EPR spectra were calculated using configurations representing the interactions between MTSL and water and the tyrosine residue 208 in the C-lobe 
Edit intent: fluency
Original: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of  Aurora-A kinase.
Revised: The understanding of kinase structure is mostly based on protein crystallography, which is limited by the requirement to trap molecules within a crystal lattice. Characterisation of the conformations of the activation loop in solution, are important to enhance the understanding of molecular processes related to diseases and to support the discovery of small molecule kinase inhibitors. In this work, molecular dynamics simulations have been employed in order to study structure and dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of Aurora-A kinase.
Edit intent: meaning-changed
Original: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of  Aurora-A kinase.
Revised: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the activation loop of Aurora-A kinase.
Edit intent: coherence
Original: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of  Aurora-A kinase.
Revised: Classical molecular dynamics (MD) simulations, within the AMBER program package that runs entirely on a CUDA-enabled NVIDIA graphic processing unit (GPU), were employed to study with low computational cost the dynamics of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase.
Edit intent: fluency
Original:  MD provided information about the conformational space of MTSL in the protein environment; an isotropic and uniform distribution of orientations of the spin label in space was found due to the large exposure of the activation loop to the solvent water.
Revised:  The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within the activation loop to the solvent water.
Edit intent: meaning-changed
Original:  an isotropic and uniform distribution of orientations of the spin label in space was found due to the large exposure of the activation loop to the solvent water. A hydrodynamic approach was employed to determine the rotational protein tumbling, while the internal motion of the spin probe was determined from 94 GHz measurements that reflect the fast motions. The theoretical 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
Revised:  an isotropic and uniform distribution of orientations of the spin label in space was found due to the large exposure of the activation loop . The 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
Edit intent: coherence
Original:  The theoretical 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
Revised:  The theoretical 9 GHz EPR spectrum of the Aurora-A kinase was measured in order to study the dynamics of the MTSL spin label attached within the activation loop, MD provided information about the different motional contributions to the overall dynamics of the MTSL and about interactions between the MTSL and the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
Edit intent: meaning-changed
Original:  The theoretical 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the MD trajectories showing the MTSL exposed to the solvent and probing the C-lobe of the protein .
Revised:  The theoretical 9 GHz EPR spectra were calculated using configurations representing interactions between MTSL and water and the tyrosine residue 208 in the C-lobe and the comparison with experimental EPR spectra produced fits that successfully reproduced the experimental spectra in agreement with the average structures obtained from the residues of the protein. Data obtained from MD were seen to be in good agreement with those obtained from QM performed in previous work and with the experimental EPR data. This work is a starting point for deeper experimental and theoretical studies of the rotational and translational diffusion properties of the Aurora-A kinase protein related to its overall tumbling and biological activity .
Edit intent: coherence
Original:  In this work,  molecular dynamics simulations have been employed in order to study structure and dynamics of the activation loop of the Aurora-A kinase . The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within the  activation loop .
Revised:  In this work, molecular dynamics simulations have been employed in order to study structure and dynamics of the activation loop of the Aurora-A kinase and of the activation loop .
Edit intent: meaning-changed
Original:  The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within the  activation loop .
Revised:  The main conformational states were determined using a clustering analysis routine within the AMBER software and the predominant modes of motion of the activation were determined performing a principal component analysis that revealed different degree of flexibility within the methane-thiosulfonate spin label, introduced into the activation loop .
Edit intent: meaning-changed