Journal of Molecular Modeling最新文献

{"title":"Molecular dynamics simulation of DNAN/DNB cocrystal PBXs","authors":"Xin-yi Li,&nbsp;Bao-guo Wang,&nbsp;Ya-fang Chen,&nbsp;Jian-bo Fu,&nbsp;Ji-hang Du,&nbsp;Chun-guang Wang","doi":"10.1007/s00894-024-06096-8","DOIUrl":"10.1007/s00894-024-06096-8","url":null,"abstract":"<div><h3>Context</h3><p>The DNAN/DNB eutectic is a high-energy explosive eutectic with superior safety and thermal stability compared to traditional melt-cast explosives. However, the addition of polymer binders can effectively enhance its mechanical properties, allowing for continued production demands without the need for changes to existing factory equipment. In this paper, a model of the DNAN/DNB eutectic explosive was established, and five different types of polymers—cis-1,4-polybutadiene (BR), ethylene–vinyl acetate copolymer (EVA), polyethylene glycol (PEG), fluorinated polymer (F2603), and polyvinylidene fluoride (PVDF)—were added to the (1 0 − 1), (1 0 1), and (0 1 1) cleavage planes, respectively, to form polymer-bonded explosives (PBXs). The stability, trigger bond length, mechanical properties, and detonation performance of the various polymer-bound PBXs were predicted retrogressively. Among the five PBX models, the DNAN/DNB/PEG model exhibited the highest binding energy and the shortest trigger bond length, indicating a significant improvement in stability, compatibility, and sensitivity compared to the original eutectic. Additionally, although the detonation performance of DNAN/DNB decreased after the addition of binders, the final results were still satisfactory. Overall, the DNAN/DNB/PEG model demonstrated excellent comprehensive performance, proving that among the many polymer binders, PEG is the optimal choice for DNAN/DNB.</p><h3>Methods</h3><p>Within the Materials Studio software, molecular dynamics (MD) simulations were employed to predict the properties of the DNAN/DNB eutectic PBX. The MD simulation timestep was set to 1 fs, with a cumulative simulation duration of 2 ns. A 2 ns MD simulation was conducted using the isothermal-isobaric ensemble (NPT). The COMPASS force field was applied, and the temperature was fixed at 295 K.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exchange-correlation kernel for perturbation dependent auxiliary functions in auxiliary density perturbation theory","authors":"Luis I. Hernández-Segura,&nbsp;Flor A. Olvera-Rubalcava,&nbsp;Roberto Flores-Moreno,&nbsp;Patrizia Calaminici,&nbsp;Andreas M. Köster","doi":"10.1007/s00894-024-06091-z","DOIUrl":"10.1007/s00894-024-06091-z","url":null,"abstract":"<div><h3>Context</h3><p>Analytic exchange-correlation kernel formulations are of the outermost importance for density functional theory (DFT) perturbation calculations. In this paper, the working equation for the exchange-correlation kernel of the generalized gradient approximation (GGA) for perturbation dependent auxiliary functions is derived and discussed in the framework of auxiliary density functional theory (ADFT). The presented new formulation is extended to the unrestricted approach, too. A comprehensive discussion of the implementation of the GGA ADFT kernel, using either the native exchange-correlation functional implementations in deMon2k or the ones from the LibXC library, is given. Calculations with analytic exchange-correlation kernels are compared to their finite difference counterparts. The obtained results are in quantitative agreement. Nevertheless, analytic GGA ADFT kernel implementations show substantial improvement in the computational performance. Similar results are reported for analytic second derivatives of effective core potential (ECP) and model core potential (MCP) matrix elements when compared to their finite difference counterparts in molecular frequency analyses.</p><h3>Method</h3><p>All calculations are performed in the framework of ADFT as implemented in deMon2k. In the ADFT analytic frequency calculations, auxiliary density perturbation theory was used. The underlying two-center exchange-correlation kernel matrix elements are calculated by numerical integration either with analytic or finite difference kernel expressions. Validation calculations are performed with the VWN and PBE functionals employing DFT-optimized DZVP basis sets in conjunction with automatically generated GEN-A2 auxiliary density function sets. In the (Pt₃Cu)_n cluster benchmark calculations, the RPBE functional was used. For Pt atoms, the quasi-relativistic LANL2DZ effective core potential with the corresponding valence basis set was employed, whereas for Cu atoms, the all-electron DFT-optimized TZVP basis was applied. The auxiliary density was expanded by the automatically generated GEN-A2* auxiliary function set. We run all benchmark calculations in parallel on 24 cores.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational insights into the structure and decomposition behaviors of 2,4,6-triamino-5-nitropyrimidine-1,3-dioxide under high pressure up to 10 GPa","authors":"Zhi-Ming Guo,&nbsp;Xi Gang,&nbsp;Xian-Zhen Jia","doi":"10.1007/s00894-024-06095-9","DOIUrl":"10.1007/s00894-024-06095-9","url":null,"abstract":"<div><h3>Context</h3><p>Inspired by the recent successful synthesis of the energetic compound 2,4,6-triamino-5-nitropyrimidine-1,3-dioxide (ICM-102), which displayed a good balance between high energy and sensitivity, the response of the structure and decomposition behaviors of ICM-102 to high pressure was systematically investigated using first principle calculations. ICM-102 exhibited a graphite-like layer structure, with the <i>c</i>-axis and the <i>a</i>-axis mainly contributing to the distance between the molecular planes. As the pressure increased from 1 atm to 10 GPa, this distance decreased from 3.166 to 2.689 Ǻ. The hydrogen bonds had the most contribution to the non-covalent interactions within the same molecular planes, resulting in the <i>b</i>-axis discontinuity. However, van der Waals interactions gradually appeared between molecular planes as the pressure increased to 2.5 GPa. Based on the analysis of crystal orbitals, the distribution of π bonds and the Laplacian bond order (LBO), it was determined that the generation mechanism of H₂O molecules involved the cleavage of N-O_c (coordinated oxygen atoms), followed by intermolecular hydrogen transfer reactions, and ultimately the formation of H₂O molecules through competition with H atoms in the amino groups within the same molecules. More importantly, the pressure dependence of LBO values for N-O_c revealed that high pressure could inhibit the ICM-102 decomposition process due to reinforcing hydrogen bonds and van der Waals interactions. This work will deepen our understanding of the stability of ICM-102 under high pressure and provide a helpful reference for its potential detonation applications.</p><h3>Methods</h3><p>All simulations, including geometry optimization and vibration analysis under quasi-hydrostatic pressure, were conducted using the CP2K code. The PBE function and the Goldk-Teter-Hutter (GTH) pseudopotential with the double-ζ-with-polarization (DZVP) basis set were employed. Additionally, the semiempirical dispersion correction D3 (BJ) was used to account for the intermolecular dispersion force. The simulations were performed under periodic boundary conditions, with a finest grid level cutoff set to 400 Ry for the Γ point. The Broyden-Flecher-Goldfarb-Shanno (BFGS) optimization method was used, with tighter convergence criteria applied for the subsequent calculations of infrared spectra. Finally, the wave-function analysis, such as non-covalent interaction and LBO, was conducted using the Multiwfn and VMD packages.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular simulation of the slurrying mechanism in microplastic semi-coke water slurry","authors":"Yuxi Liu,&nbsp;Zhiyuan Yang,&nbsp;Xiaoqian Ju,&nbsp;Baolu Cui,&nbsp;Jingwen Wang,&nbsp;Dechao Wang,&nbsp;Zhiping Chen,&nbsp;Anning Zhou","doi":"10.1007/s00894-024-06100-1","DOIUrl":"10.1007/s00894-024-06100-1","url":null,"abstract":"<div><h3>Context</h3><p>This study explores the interaction between particles in microplastic semi-coke water slurry at the molecular level using molecular simulation methods, specifically DFT calculations and MD simulations. In addition, the experiment of slurry preparation was carried out to study the viscosity and stability of the slurry. The electrostatic potential analysis shows that the interaction between microplastics and dispersant molecules occurs on atoms with large electronegativity or oxygen-containing functional groups, and the energy gap of frontier molecular orbitals indicated that PVC interacts most easily with the dispersant (0.39 eV), followed by PS (1.08 eV) and PET (3.65 eV). In addition, it is also noted that due to the steric hindrance effect, the adsorption energy was opposite to the DFT calculation results: PET was − 213.338 kcal/mol (NNO) which was highest, followed by PS (− 107.603 kcal/mol, NNO), and PVC (NNO) was lowest which was − 94.808 kcal/mol. And RDF shows similar results, which the probability of water molecules in the PET system was the highest, followed by PS, and finally, PVC. The MD results are consistent with the viscosity and stability characterization results of the slurry which PET has the lowest viscosity of 87.3 mPa·s. Finally, this study provides new ideas for the treatment of microplastics and the improvement of the performance of semi-coke water slurry and reveals the interaction mechanism between microplastics and semi-coke water slurry.</p><h3>Methods</h3><p>All calculations were performed using Materials Studio (MS) version 2020 software, BIOVIA Corporation. The DFT calculation was carried out through the DMol³ module. The DFT calculations include electron density, electrostatics, orbitals, and population analysis. In DMol³ module, the GGA-PBE function was selected to consider gradient changes in density in the simulated calculation. The DFT-D correction was selected, and all electrons were calculated by DNP for accurate core potentials and the DNP file was 4.4. MD simulation was performed through the Forcite module. MD simulation mainly focuses on relative concentration distribution analysis, radial distribution function, and adsorption energy calculation. All molecular geometry optimizations are performed in the Forcite module. In the molecular dynamic part, all simulations used PCFF forcefield. The NVT ensemble was adopted and using the Nosé thermostat.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correspondence between the reaction force minimum and the onset of abrupt variations of the kinetic and potential energies in bond dissociation and formation","authors":"Peter Politzer,&nbsp;Soledad Gutiérrez-Oliva,&nbsp;Timothy Clark,&nbsp;Jane S. Murray","doi":"10.1007/s00894-024-06101-0","DOIUrl":"10.1007/s00894-024-06101-0","url":null,"abstract":"<div><h3>Context</h3><p>We demonstrate that the minimum of the reaction force curve of a diatomic or polyatomic molecule undergoing bond dissociation is significant in several respects. As has been pointed out in the past, it is the point at which the force opposing dissociation is strongest. It marks the boundary between the primarily structural stage of a bond dissociation (stretching) and the transition region between the stretched bond and independent atoms. We now show that the reaction force minimum is also where the kinetic and potential energy curves tend to change direction abruptly. At this point, the total energy E(R) has increased by about 27% of the dissociation energy, for both diatomic and polyatomic molecules.</p><h3>Methods</h3><p>Dissociation curves are analyzed at the UHF/daug-cc-pV5Z level of theory using Gaussian 16.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theoretical insight into physical characteristics of lead-free perovskites Rb2TlSbX6 (X = Cl, Br, I) for optoelectronic devices","authors":"Ibrar Ali Shah,&nbsp;Muhammad Imran,&nbsp;Fayyaz Hussain,&nbsp;Umbreen Rasheed,&nbsp;Manawwer Alam,&nbsp;Syed Mansoor Ali,&nbsp;Rizwan Wahab,&nbsp;R. M. A. Khalil,&nbsp;Muhammad Fahad Ehsan,&nbsp;Muhammad Shoaib","doi":"10.1007/s00894-024-06092-y","DOIUrl":"10.1007/s00894-024-06092-y","url":null,"abstract":"<div><h3>Context</h3><p>Novel optoelectronic and thermoelectric properties with broad compositional range, non-toxic nature and structural stability make halide-based double perovskites fascinating for flexible optoelectronic devices. In this work, the structural electronic, optical and transport properties of Rb₂TlSbX₆ (X = Cl, Br, I) were studied using density functional theory for optoelectronic devices. The elastic analysis demonstrates ductile nature, mechanical stability, anisotropic behaviour and feasibility for flexible optoelectronic devices. The band structure study using Tran–Blaha–modified Becke–Johnson (TB-mBJ) potential shows that all studied materials have direct bandgap. In addition, the bandgap of Rb₂TlSbCl₆ is more appropriate for optoelectronic devices. The small loss and maximum absorption in visible regions make these materials prime candidates for optoelectronic devices. The transport features indicate that all the studied double perovskites reflect p-type semiconducting behaviour as highlighted by positive Seebeck coefficient values. Furthermore, the high power factor values of Rb₂TlSbX₆ (X = Cl, Br, I) double perovskites make them suitable for thermoelectric device applications at high temperatures. Based on electronic optical and thermoelectric properties Rb₂TlSbCl₆ is the best candidate for flexible optoelectronic devices.</p><h3>Methods</h3><p>In this paper, structural optimization of Rb₂TlSbX₆ (X = Cl, Br, I) double perovskites was conducted utilizing the Wien2k software based on first principle calculations with Perdew-Burke-Ernzerhof’s generalized-gradient approximation (PBE-sol approximation). The TB-mBJ potential was employed to compute the accurate band gap of studied materials. The thermoelectric properties are evaluated with BoltzTraP code, showing a predominance of P-type charge carriers in all studied perovskites. This methodological strategy verifies the material’s remarkable stability and optical properties and offers a solid framework for examining its potential in optoelectronic devices.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141896428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis","authors":"Venkata N. Are,&nbsp;Rajarshi Roy,&nbsp;Sandeep Kumar Dhanda,&nbsp;Sanchit Neema,&nbsp;Neha Rani Sahu,&nbsp;Nitin Adithya,&nbsp;Ritudhwaj Tiwari,&nbsp;Parimal Kar,&nbsp;Debasis Nayak","doi":"10.1007/s00894-024-06088-8","DOIUrl":"10.1007/s00894-024-06088-8","url":null,"abstract":"<div><h3>Context</h3><p>Flaviviruses cause severe encephalitic or hemorrhagic diseases in humans. Its members, Kyasanur forest disease virus (KFDV) and Alkhumra hemorrhagic fever virus (ALKV), cause hemorrhagic fever and are prevalent in India and Saudi Arabia, respectively, while the tick-borne encephalitis virus (TBEV) causes a dangerous encephalitic infection in Europe and Asia. However, little information is available about the targets of immune responses for these deadly viruses. Here, we predict potential antigenic peptide epitopes of viral envelope protein for inducing a cell-mediated and humoral immune response.</p><h3>Methods</h3><p>Using the Immune Epitope Database and Analysis Resource (IEDB-AR), we identified 13 MHC-I and two MHC-II dominant conserved epitopes in KFDV and ALKV and six MHC-I and three MHC-II epitopes in TBEV envelope proteins. Parallelly, we also predicted B-cell linear and discontinuous envelope protein epitopes for these viruses. Interestingly, the epitopes are conserved in all three viral envelope proteins. Further, the discontinuous epitopes are structurally compared with the available DENV, ZIKV, WNV, TBEV, and LIV envelope protein antibody structures. Overall structural comparison analyses highlight (i) lateral ridge epitope in the ED-III domain of E protein, and (ii) envelope dimer epitope (EDE) could be targeted for developing potent vaccine candidates as well as therapeutic antibody production. Moreover, existing structural and biochemical functions of the same epitopes in homologous viruses are predicted to have a reduced antibody-dependent enhancement (ADE) effect on flaviviral infection.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phographene as a new carbon allotrope for adsorption and detection of SO2, AsH3, NO2, CF3H, and CO2 air pollutant gaseous species","authors":"Anupam Yadav,&nbsp;Mohammed Ahmed Mustafa,&nbsp;Amina Dawood Suleman,&nbsp;Karar R. Al-Shami,&nbsp;Morug Salih Mahdi,&nbsp;Ahmed Read Al-Tameemi,&nbsp;Montather F. Ramadan,&nbsp;Zainab Sadeq Yousif,&nbsp;Raheem Joui,&nbsp;Shahad Abdulhadi Khuder,&nbsp;Merwa Alhadrawi","doi":"10.1007/s00894-024-06063-3","DOIUrl":"10.1007/s00894-024-06063-3","url":null,"abstract":"<div><h3>Context \u0000</h3><p>Phographene and its family member structures are of the newly proposed semiconductors for detection of chemicals. That is, in this project, the potential of using α-phographene (α-POG) both for adsorption and detection of five types of the most important air pollutant gases containing SO₂, AsH₃, CF₃H, NO₂, and CO₂ species were investigated.  The results of the time dependent density functional theory (TD-DFT) calculations indicate that during the adsorption of NO₂, and SO₂ by the sorbent, big redshifts occur (up to 866.2 nm, and 936.5, respectively) resulting in considerable changes in the orbitals and the electronic structures of the systems. Moreover, the results of the thermodynamic calculations reveal that α-POG could selectively adsorb SO₂, NO₂, and AsH3 gases (with different orders), but it could not adsorb the two other gases.Finally, the outcome of the band gap calculations shows that between all mentioned gases, α-POG could selectively detect the presence of SO₂, and then NO₂; while, this nanosheet could not sense the existence of AsH₃, CF₃H, or CO₂ gases.</p><h3>Methods</h3><p>All of the calculations were carried out by using the Gaussian 03 quantum chemical package. In addition, the physiochemical parameters were extracted from the output files for further calculations. Studies on all saddle points and the following calculations were performed applying the B3LYP/6-311g(d,p) level of theory. \u0000</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141858714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A DFT study on the heterolytic bond cleavage of hydrazones under cathodic conditions in acetonitrile","authors":"Mark A. W. Lawrence","doi":"10.1007/s00894-024-06082-0","DOIUrl":"10.1007/s00894-024-06082-0","url":null,"abstract":"<div><h3>Context</h3><p>Hydrazones have been studied for a myriad of chemical and physiochemical properties, such as sensors, chelators and numerous biological activities. Experimental data indicates that hydrazones are unstable under cathodic potentials irrespective of the solvent. The single electron reduction of hydrazones to produce radical anions result in unstable species that cleaves at the N–N bond in a heterolytic manner. The literature has proposed a mechanism favouring the radical on the imine moiety, however in this study DFT calculations suggest the radical on the amine product is more likely upon bond cleavage. This has implications on electrochemical mechanisms, and the active molecule in biological studies viz the method of delivery to target areas.</p><h3>Methods</h3><p>Density functional theory calculations were carried out using the GAMESS software package. The structures were optimized in the gas phase (B3LYP/6-31G(d,p)) as indicated by the absence of imaginary frequencies in the Hessian, and in CH₃CN (B3LYP/6-31G(d,p)/SMD) with the Pople polarization functions. As a comparison, selected pathways were fully optimized using PBE0/6-31G(d,p) and PBE0/6-31G(d,p)/SMD for gas phase and CH₃CN, respectively with the Pople polarization functions. The values were not significantly different (&lt; 5% difference). As such only the B3LYP is evaluation is discussed.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DRML-Ensemble: drug repurposing method based on feature construction of multi-layer ensemble","authors":"Mengfei Zhang,&nbsp;Hongjian He,&nbsp;Jiang Xie,&nbsp;Qing Nie","doi":"10.1007/s00894-024-06087-9","DOIUrl":"10.1007/s00894-024-06087-9","url":null,"abstract":"<div><h3>Context</h3><p>Computational drug repurposing methods have been continuously developed in recent years to alleviate the high costs associated with drug development. As drug targets or the products of disease-related genes, proteins play an important role in drug repurposing. Although the potential has been demonstrated, heterogeneous graphs with proteins as independent nodes have yet to be studied, where extracting high-quality protein features from heterogeneous graphs poses a significant challenge. A novel drug repurposing model based on the feature construction of multi-layer ensemble (DRML-Ensemble) is proposed in this study. The performance of DRML-Ensemble, as evaluated on publicly available datasets, achieves an AUPR value of 0.93 and an AUROC value of 0.92, surpassing those of existing state-of-the-art methods. Additionally, DRML-Ensemble demonstrates its notable ability for drug repurposing in Alzheimer’s disease.</p><h3>Methods</h3><p>DRML-Ensemble is primarily composed of multiple layers of heterogeneous graph feature construction (HGFC). Each HGFC can extract protein features by leveraging the relationships between drugs, diseases, and proteins. These protein features are then utilized in subsequent layers to build drug and disease features, facilitating drug repurposing. By stacking multiple layers, optimal protein features can be obtained from the heterogeneous graph, consequently improving the accuracy of drug repurposing. However, an excessive· stacking of layers usually affect the model’s training process, for example, causing problems such as overfitting; a multi-layer ensemble prediction module is designed to further improve the model’s performance.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":null,"pages":null},"PeriodicalIF":2.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}