Accurately estimating protein–ligand binding free energy is crucial for drug design and biophysics, yet remains a challenging task. In this study, we applied the screening molecular mechanics/Poisson–Boltzmann surfa...Accurately estimating protein–ligand binding free energy is crucial for drug design and biophysics, yet remains a challenging task. In this study, we applied the screening molecular mechanics/Poisson–Boltzmann surface area(MM/PBSA)method in combination with various machine learning techniques to compute the binding free energies of protein–ligand interactions. Our results demonstrate that machine learning outperforms direct screening MM/PBSA calculations in predicting protein–ligand binding free energies. Notably, the random forest(RF) method exhibited the best predictive performance,with a Pearson correlation coefficient(rp) of 0.702 and a mean absolute error(MAE) of 1.379 kcal/mol. Furthermore, we analyzed feature importance rankings in the gradient boosting(GB), adaptive boosting(Ada Boost), and RF methods, and found that feature selection significantly impacted predictive performance. In particular, molecular weight(MW) and van der Waals(VDW) energies played a decisive role in the prediction. Overall, this study highlights the potential of combining machine learning methods with screening MM/PBSA for accurately predicting binding free energies in biosystems.展开更多
Poly(glycolic acid)(PGA)is derived from glycolide obtained by fermenting pineapples or sugarcane,which has excellent gas barrier properties and a small carbon footprint.PGA is a potential substitute for the current al...Poly(glycolic acid)(PGA)is derived from glycolide obtained by fermenting pineapples or sugarcane,which has excellent gas barrier properties and a small carbon footprint.PGA is a potential substitute for the current aluminum-plastic composite films used in high barrier packaging applications.However,its poor ductility and narrow processing window limit its application in food packaging.Herein,poly(butylene succinate-co-butylene adipate)(PBSA)was used to fabricate PGA/PBSA blend films through an in situ fibrillation technique and blown film extrusion.Under the elongational flow field used during the extrusion process,a unique hierarchical structure based on the PBSA nanofibrils and interfacially oriented PGA crystals was obtained.This structure enhances the strength,ductility and gas barrier properties of the PGA/PBSA blend film.In addition,an epoxy chain extender(ADR4468)was used as a compatibilizer to further enhance the interfacial adhesion between PGA and PBSA.70PGA/0.7ADR exhibited a very low oxygen permeability(2.34×10^(-4)Barrer)with significantly high elongating at break(604.4%),tensile strength(47.4 MPa),and transparency,which were superior to those of petroleum-based polymers.Thus,the 70PGA/0.7ADR blown films could satisfy the requirements for most instant foods such as coffee,peanuts,and fresh meat.展开更多
Poly(butylene adipate-co-terephthalate)(PBAT)and poly(butylene succinate-co-adipate)(PBSA)blend films were prepared with different contents of a multifunctional epoxide chain extender Joncryl ADR-4468(ADR)or benzoyl p...Poly(butylene adipate-co-terephthalate)(PBAT)and poly(butylene succinate-co-adipate)(PBSA)blend films were prepared with different contents of a multifunctional epoxide chain extender Joncryl ADR-4468(ADR)or benzoyl peroxide(BPO).The long-chain-branching(LCB)introduced by ADR and branched/crosslinked entanglement induced by BPO increased melt elasticity,viscosity and compatibility,as indicated by thermal properties,rheological and morphological analyses.It was found that the elongation at break and the tensile strength were significantly improved,due to the enhancement of compatibility and the interfacial adhesion by the incorporation of ADR or BPO.The best mechanical properties were obtained in PBAT/PBSA/ADR(60/40/0.3)(A4T6A_(0.3))and PBAT/PBSA/BPO(60/40/0.9)(A4T6B_(0.9))films,respectively.With the rapid initiation of chain growth by BPO,it has significantly improved the transparency of the film.ADR and BPO can be used interchangeably in improving the comprehensive properties of PBAT/PBSA films,and it would provide more strategies for developing biodegradable materials for various applications.展开更多
The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding ene...The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.展开更多
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 12222506, 12347102, 12447164, and 12174184)。
文摘Accurately estimating protein–ligand binding free energy is crucial for drug design and biophysics, yet remains a challenging task. In this study, we applied the screening molecular mechanics/Poisson–Boltzmann surface area(MM/PBSA)method in combination with various machine learning techniques to compute the binding free energies of protein–ligand interactions. Our results demonstrate that machine learning outperforms direct screening MM/PBSA calculations in predicting protein–ligand binding free energies. Notably, the random forest(RF) method exhibited the best predictive performance,with a Pearson correlation coefficient(rp) of 0.702 and a mean absolute error(MAE) of 1.379 kcal/mol. Furthermore, we analyzed feature importance rankings in the gradient boosting(GB), adaptive boosting(Ada Boost), and RF methods, and found that feature selection significantly impacted predictive performance. In particular, molecular weight(MW) and van der Waals(VDW) energies played a decisive role in the prediction. Overall, this study highlights the potential of combining machine learning methods with screening MM/PBSA for accurately predicting binding free energies in biosystems.
基金the National Key Research and Development Program of China(No.2022YFB3704900)the National Natural Science Foundation of China(No.52073004)China National Tobacco Corporation Guizhou Company(No.2023XM24)。
文摘Poly(glycolic acid)(PGA)is derived from glycolide obtained by fermenting pineapples or sugarcane,which has excellent gas barrier properties and a small carbon footprint.PGA is a potential substitute for the current aluminum-plastic composite films used in high barrier packaging applications.However,its poor ductility and narrow processing window limit its application in food packaging.Herein,poly(butylene succinate-co-butylene adipate)(PBSA)was used to fabricate PGA/PBSA blend films through an in situ fibrillation technique and blown film extrusion.Under the elongational flow field used during the extrusion process,a unique hierarchical structure based on the PBSA nanofibrils and interfacially oriented PGA crystals was obtained.This structure enhances the strength,ductility and gas barrier properties of the PGA/PBSA blend film.In addition,an epoxy chain extender(ADR4468)was used as a compatibilizer to further enhance the interfacial adhesion between PGA and PBSA.70PGA/0.7ADR exhibited a very low oxygen permeability(2.34×10^(-4)Barrer)with significantly high elongating at break(604.4%),tensile strength(47.4 MPa),and transparency,which were superior to those of petroleum-based polymers.Thus,the 70PGA/0.7ADR blown films could satisfy the requirements for most instant foods such as coffee,peanuts,and fresh meat.
基金supported by Science and Technology Support Plan of Suqian(H201510)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)Nanjing Wurui Biodegradable Materials Research Institute.
文摘Poly(butylene adipate-co-terephthalate)(PBAT)and poly(butylene succinate-co-adipate)(PBSA)blend films were prepared with different contents of a multifunctional epoxide chain extender Joncryl ADR-4468(ADR)or benzoyl peroxide(BPO).The long-chain-branching(LCB)introduced by ADR and branched/crosslinked entanglement induced by BPO increased melt elasticity,viscosity and compatibility,as indicated by thermal properties,rheological and morphological analyses.It was found that the elongation at break and the tensile strength were significantly improved,due to the enhancement of compatibility and the interfacial adhesion by the incorporation of ADR or BPO.The best mechanical properties were obtained in PBAT/PBSA/ADR(60/40/0.3)(A4T6A_(0.3))and PBAT/PBSA/BPO(60/40/0.9)(A4T6B_(0.9))films,respectively.With the rapid initiation of chain growth by BPO,it has significantly improved the transparency of the film.ADR and BPO can be used interchangeably in improving the comprehensive properties of PBAT/PBSA films,and it would provide more strategies for developing biodegradable materials for various applications.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11874045 and 11774147)。
文摘The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.
