Motivation Protein glycosylation is one of the most abundant post-translational modifications tha... more Motivation Protein glycosylation is one of the most abundant post-translational modifications that plays an important role in immune responses, intercellular signaling, inflammation and host-pathogen interactions. However, due to the poor ionization efficiency and microheterogeneity of glycopeptides identifying glycosylation sites is a challenging task, and there is a demand for computational methods. Here, we constructed the largest dataset of human and mouse glycosylation sites to train deep learning neural networks and support vector machine classifiers to predict N-/O-linked glycosylation sites, respectively. Results The method, called SPRINT-Gly, achieved consistent results between ten-fold cross validation and independent test for predicting human and mouse glycosylation sites. For N-glycosylation, a mouse-trained model performs equally well in human glycoproteins and vice versa, however, due to significant differences in O-linked sites separate models were generated. Overall,...
Equilibrium molecular dynamics simulation techniques are used to obtain accurate compressibility ... more Equilibrium molecular dynamics simulation techniques are used to obtain accurate compressibility factors (⩽0·1% error) for tangent hard-sphere (THS) chains of lengths 2–8, 16, 32, 64, 96, and 192. Our simulation results show that, within simulation statistical errors, the dependence of compressibility factors on chain length approaches linearity very rapidly. At volume fractions of 0·4 or above the linearity starts at a chain length of 3, while at volume fractions of 0·1 or above the linearity starts at a chain length of 6. The thermodynamic perturbation theory (TPT) and the generalized Flory (GF) theory equations of state are extended to become a linear combination of the compressibility factors of any two reference THS chain fluids. It is found that extended GF theory is identical to extended TPT when the excluded volumes of chains and reference chains are assumed to be linearly dependent on the chain length. Our simulation data implies that a near exact THS chain equation of state can be obtained from ...
Exact results for the thermodynamic properties of isolated freely jointed sticky trimers and tetr... more Exact results for the thermodynamic properties of isolated freely jointed sticky trimers and tetramers are obtained by taking appropriate limits on the exact results for a single square-well chain. Two new methods for approximating the square-well potential by a sticky potential are suggested. These new methods extend greatly the range of square-well widths over which the thermodynamic properties of a single square-well chain can be estimated accurately in terms of the corresponding properties of a single sticky chain.
A theorem for convolution integrals is proved and then applied to extend the “second zero-separat... more A theorem for convolution integrals is proved and then applied to extend the “second zero-separation theorem” to the bridge functionb(r) and direct-correlation tail functionsd(r). This theorem allows us to exactly relate∂b(r)/∂r and∂d(r)/∂ratr=0 for the hard-sphere fluid to the “contact value” of the radial distribution functiong(r) atr=σ+. From this we obtain immediately the exact values of ∂b(r)/∂r and ∂d(r)/∂r atr=0 through second order in number density ρ. Using our results to compare the exact and Percus-Yevick (PY) bridge function, we find that they differ significantly. After obtaining the bridge function and tail function and their derivatives atr=0 andr=σ through, we suggest new approximations forb(0) andd(0) as well as an analytical integral-equation theory to improve the PY approximation in the pure hard-sphere fluid. The major deficiency of that approximation has been its poor assessment of the cavity function inside the hard-core region. Our theory remedies this defect in a way that yields ay(r) that is self-consistent with respct to the virial and compressibility relations and also the two zero-separation relations involvingy(r) and its spatial derivative atr=0.
A formally exact nonlocal density-functional expansion procedure for direct correlation functions... more A formally exact nonlocal density-functional expansion procedure for direct correlation functions developed earlier by Stell for a homogeneous system, and extended by Blum and Stell, Sullivan and Stell, and ourselves to various inhomogeneous systems, is used here to derive nonlocal integral-equation approximations. Two of the simplest of these approximations (zeroth order), which we shall characterize here as the hydrostatic Percus–Yevick
The Born solvation free energy (BSFE) of two ions at a fixed distance from one another in a model... more The Born solvation free energy (BSFE) of two ions at a fixed distance from one another in a model polar solvent is obtained via two approaches. In the interaction‐site approach, the two ions are modeled as a rigid extended dipolar dumbbell. Analytical expressions for the BSFE for such a dumbbell model in a dipolar dumbbell and a dipolar hard‐sphere solvent are obtained under a mean spherical approximation (MSA). In the second approach, a thermodynamic cycle is established such that the BSFE for two ions a fixed distance apart can be expressed in terms of the solvent‐averaged potential between the two ions and other known quantities. The results obtained via these two approaches are reasonably consistent, with the thermodynamic‐cycle BSFE as a function of distance exhibiting more of the structure one expects to find in a molecular solvent. Both BSFE functions are substantially different from the corresponding continuum‐solvent result. When the distance between two ions goes to infinity, our results reduce ...
Analytical equations are obtained for the pair correlation functions in the mean spherical approx... more Analytical equations are obtained for the pair correlation functions in the mean spherical approximation (MSA) for two charged hard‐sphere ions in a model molecular solvent. Model solvents of dipolar dumbbells (which may be partially dissociative) or charged hard‐spheres fused in a tetrahedral configuration are treated in an extended MSA. The resulting expressions for the Born solvation free energy of an ion are very similar to that obtained earlier by Chan et al. for a charged hard‐sphere ion in a dipolar hard‐sphere solvent. The solvent averaged ion–ion potentials are obtained in the hypernetted chain approximation. Comparisons among results of various solvents are also made. In order of increasing oscillation amplitudes of the solvent averaged ion–ion potential for given molecular density and dipole moment we have continuum ≪dumbbell≤tetrahedral
The pairing mean spherical approximation (PMSA) developed in the previous paper of this series is... more The pairing mean spherical approximation (PMSA) developed in the previous paper of this series is applied to a binary mixture of hard spheres and ions of the restricted primitive model. The resulting equation of state is used to investigate the phase equilibrium for the binary mixture. It is found that the model exhibits type‐III phase behavior. This work serves as the basis for more realistic models.
Motivation Protein glycosylation is one of the most abundant post-translational modifications tha... more Motivation Protein glycosylation is one of the most abundant post-translational modifications that plays an important role in immune responses, intercellular signaling, inflammation and host-pathogen interactions. However, due to the poor ionization efficiency and microheterogeneity of glycopeptides identifying glycosylation sites is a challenging task, and there is a demand for computational methods. Here, we constructed the largest dataset of human and mouse glycosylation sites to train deep learning neural networks and support vector machine classifiers to predict N-/O-linked glycosylation sites, respectively. Results The method, called SPRINT-Gly, achieved consistent results between ten-fold cross validation and independent test for predicting human and mouse glycosylation sites. For N-glycosylation, a mouse-trained model performs equally well in human glycoproteins and vice versa, however, due to significant differences in O-linked sites separate models were generated. Overall,...
Equilibrium molecular dynamics simulation techniques are used to obtain accurate compressibility ... more Equilibrium molecular dynamics simulation techniques are used to obtain accurate compressibility factors (⩽0·1% error) for tangent hard-sphere (THS) chains of lengths 2–8, 16, 32, 64, 96, and 192. Our simulation results show that, within simulation statistical errors, the dependence of compressibility factors on chain length approaches linearity very rapidly. At volume fractions of 0·4 or above the linearity starts at a chain length of 3, while at volume fractions of 0·1 or above the linearity starts at a chain length of 6. The thermodynamic perturbation theory (TPT) and the generalized Flory (GF) theory equations of state are extended to become a linear combination of the compressibility factors of any two reference THS chain fluids. It is found that extended GF theory is identical to extended TPT when the excluded volumes of chains and reference chains are assumed to be linearly dependent on the chain length. Our simulation data implies that a near exact THS chain equation of state can be obtained from ...
Exact results for the thermodynamic properties of isolated freely jointed sticky trimers and tetr... more Exact results for the thermodynamic properties of isolated freely jointed sticky trimers and tetramers are obtained by taking appropriate limits on the exact results for a single square-well chain. Two new methods for approximating the square-well potential by a sticky potential are suggested. These new methods extend greatly the range of square-well widths over which the thermodynamic properties of a single square-well chain can be estimated accurately in terms of the corresponding properties of a single sticky chain.
A theorem for convolution integrals is proved and then applied to extend the “second zero-separat... more A theorem for convolution integrals is proved and then applied to extend the “second zero-separation theorem” to the bridge functionb(r) and direct-correlation tail functionsd(r). This theorem allows us to exactly relate∂b(r)/∂r and∂d(r)/∂ratr=0 for the hard-sphere fluid to the “contact value” of the radial distribution functiong(r) atr=σ+. From this we obtain immediately the exact values of ∂b(r)/∂r and ∂d(r)/∂r atr=0 through second order in number density ρ. Using our results to compare the exact and Percus-Yevick (PY) bridge function, we find that they differ significantly. After obtaining the bridge function and tail function and their derivatives atr=0 andr=σ through, we suggest new approximations forb(0) andd(0) as well as an analytical integral-equation theory to improve the PY approximation in the pure hard-sphere fluid. The major deficiency of that approximation has been its poor assessment of the cavity function inside the hard-core region. Our theory remedies this defect in a way that yields ay(r) that is self-consistent with respct to the virial and compressibility relations and also the two zero-separation relations involvingy(r) and its spatial derivative atr=0.
A formally exact nonlocal density-functional expansion procedure for direct correlation functions... more A formally exact nonlocal density-functional expansion procedure for direct correlation functions developed earlier by Stell for a homogeneous system, and extended by Blum and Stell, Sullivan and Stell, and ourselves to various inhomogeneous systems, is used here to derive nonlocal integral-equation approximations. Two of the simplest of these approximations (zeroth order), which we shall characterize here as the hydrostatic Percus–Yevick
The Born solvation free energy (BSFE) of two ions at a fixed distance from one another in a model... more The Born solvation free energy (BSFE) of two ions at a fixed distance from one another in a model polar solvent is obtained via two approaches. In the interaction‐site approach, the two ions are modeled as a rigid extended dipolar dumbbell. Analytical expressions for the BSFE for such a dumbbell model in a dipolar dumbbell and a dipolar hard‐sphere solvent are obtained under a mean spherical approximation (MSA). In the second approach, a thermodynamic cycle is established such that the BSFE for two ions a fixed distance apart can be expressed in terms of the solvent‐averaged potential between the two ions and other known quantities. The results obtained via these two approaches are reasonably consistent, with the thermodynamic‐cycle BSFE as a function of distance exhibiting more of the structure one expects to find in a molecular solvent. Both BSFE functions are substantially different from the corresponding continuum‐solvent result. When the distance between two ions goes to infinity, our results reduce ...
Analytical equations are obtained for the pair correlation functions in the mean spherical approx... more Analytical equations are obtained for the pair correlation functions in the mean spherical approximation (MSA) for two charged hard‐sphere ions in a model molecular solvent. Model solvents of dipolar dumbbells (which may be partially dissociative) or charged hard‐spheres fused in a tetrahedral configuration are treated in an extended MSA. The resulting expressions for the Born solvation free energy of an ion are very similar to that obtained earlier by Chan et al. for a charged hard‐sphere ion in a dipolar hard‐sphere solvent. The solvent averaged ion–ion potentials are obtained in the hypernetted chain approximation. Comparisons among results of various solvents are also made. In order of increasing oscillation amplitudes of the solvent averaged ion–ion potential for given molecular density and dipole moment we have continuum ≪dumbbell≤tetrahedral
The pairing mean spherical approximation (PMSA) developed in the previous paper of this series is... more The pairing mean spherical approximation (PMSA) developed in the previous paper of this series is applied to a binary mixture of hard spheres and ions of the restricted primitive model. The resulting equation of state is used to investigate the phase equilibrium for the binary mixture. It is found that the model exhibits type‐III phase behavior. This work serves as the basis for more realistic models.
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Papers by Yaoqi Zhou