Journal of molecular graphics & modelling最新文献_第3页

Density functional theory and molecular dynamics simulation of water molecules confined between two-dimensional graphene oxide surfaces 封闭在二维氧化石墨烯表面之间的水分子的密度泛函理论和分子动力学模拟

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-09-12 DOI: 10.1016/j.jmgm.2024.108862

{"title":"Density functional theory and molecular dynamics simulation of water molecules confined between two-dimensional graphene oxide surfaces","authors":"","doi":"10.1016/j.jmgm.2024.108862","DOIUrl":"10.1016/j.jmgm.2024.108862","url":null,"abstract":"<div>In this work, the interaction potentials of water molecule with the two-dimensional graphene oxide (GO) surfaces containing epoxy groups have been determined using the M06–2X/6-31g (d,p) level of theory at different orientations and separations and fitted to the Born-Huggins-Meyer (BHM) potential. Good agreements were found between the computed and the well-known OPLS-AA and Dreiding potentials. We have also used some calculated potentials and the well-known models in the molecular dynamics (MD) simulations. Our results showed that some of the calculated force fields for both 2D GO structures almost represent similar results of average number of hydrogen bonds (<HB>), radial distribution functions (RDF), self-diffusion coefficient, and angle distribution function (ADF) with the OPLS-AA and Dreiding models which are due to their agreements of the interaction potentials. However, some models in both GO systems represent different results because of their shifted potentials to the larger distances. Our results also showed that the confined water molecules tend to orient toward the epoxy groups on the GO surfaces and the distributions at the angles of θ = 0o (or θ = 180o) is more than the other distributions. The water molecules confined between the bent GO surfaces showed less diffusion coefficients than the flat structure.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142241974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

First-principle calculations to investigate mechanical and acoustical properties of predicted stable halide Perovskite ABX3 通过第一原理计算研究预测的稳定卤化物 Perovskite ABX3 的机械和声学特性

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-09-10 DOI: 10.1016/j.jmgm.2024.108861

{"title":"First-principle calculations to investigate mechanical and acoustical properties of predicted stable halide Perovskite ABX3","authors":"","doi":"10.1016/j.jmgm.2024.108861","DOIUrl":"10.1016/j.jmgm.2024.108861","url":null,"abstract":"<div>This work examines the predicted stable halide perovskites' elastic, acoustical, and thermal characteristics. The work uses the Full Potential-Linearized Augmented Plane Wave (FP-LAPW) technique through PBE-GGA to compute compounds in the WIEN2K algorithm. The ELATE program for the evaluation of elastic tensors to plot 2D and 3D graphs was also used. The bulk modulus, Young's modulus, shear modulus, anisotropy factors, Cauchy pressure, Pugh's ratio, Poisson's ratio, Kleinman's parameter, Lame's coefficient, Vicker's hardness, sound velocities, Gruneisen parameter and even melting and Debye temperature were computed. The mechanical and elastic properties are reported for the first time for most of the compounds, demonstrating that the investigated HPs—aside from TlBeF3, BaAgBr3, and CsTcl3—are mechanically stable and exhibit weaker resistance against shear distortion than they do to unidirectional compression. The results of Poisson's, Pugh's, and Frantsevich's ratios data prove that all materials are ductile except SrLiF3. The estimated Poisson's ratio data indicates the metallic bonding nature of HPs, whereas only SrLiF3 exhibits covalent behavior with ν = 0.23. Debye temperature for SrLiF3, ZnLiF3, ZnScF3, CsRhCl3, CsRuCl3, and CsBeCl3 is greater than 200 K which signifies their hardness, thermal conductivity, and high sound velocities. The large melting temperature values, make them suitable for high-temperature industrial applications. The anharmonicity effect is highest for CaCuBr3 (3.265) and lowest for SrLiF3 (1.402). The current approach calculates elastic and mechanical properties, providing a practical understanding of various physical processes and enabling technology developers to utilize compounds in diverse applications.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular dynamics simulation study of graphene synthesis by rotating arc plasma 旋转电弧等离子体合成石墨烯的分子动力学模拟研究

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-09-03 DOI: 10.1016/j.jmgm.2024.108849

{"title":"Molecular dynamics simulation study of graphene synthesis by rotating arc plasma","authors":"","doi":"10.1016/j.jmgm.2024.108849","DOIUrl":"10.1016/j.jmgm.2024.108849","url":null,"abstract":"<div>The rotating arc plasma method, based on its unique characteristics, provides a simple, efficient, and catalyst-free approach for graphene material synthesis. This study employs molecular dynamics simulations to theoretically investigate the detailed growth process of graphene at the atomic scale using plasma. During the growth process, different radicals serve as dissociation precursors within the plasma. Simulation results indicate that the growth process of graphene clusters involves three stages: extension of carbon clusters, cyclization of carbon chains, and coalescence of clusters into sheets. Firstly, the precursor concentration affects the size of graphene clusters; increasing the precursor concentration enlarges the cluster size but also increases the likelihood of curling. Secondly, increasing the hydrogen content in the precursor can reduce the growth rate of clusters, decrease dangling bonds at the periphery of clusters, thereby slowing down cluster closure and maintaining a well-defined sheet structure. Lastly, appropriately elevating the simulation temperature can enhance the reaction rate during the simulation process without altering the reaction pathway. These research findings establish the foundation for understanding the growth mechanism of graphene.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142228559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of potential inhibitors against Corynebacterium diphtheriae MtrA response regulator protein; an in-silico drug discovery approach 鉴定白喉棒状杆菌 MtrA 反应调节蛋白的潜在抑制剂；一种在实验室中发现药物的方法。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-09-01 DOI: 10.1016/j.jmgm.2024.108858

{"title":"Identification of potential inhibitors against Corynebacterium diphtheriae MtrA response regulator protein; an in-silico drug discovery approach","authors":"","doi":"10.1016/j.jmgm.2024.108858","DOIUrl":"10.1016/j.jmgm.2024.108858","url":null,"abstract":"<div>Corynebacterium diphtheriae is a multi-drug resistant bacteria responsible for the life-threatening respiratory illness, diphtheria which can lead to severe Nervous system disorders, mainly infecting the lungs, heart, and kidneys if left untreated. In the current study, Corynebacterium diphtheriae MtrA response regulator protein was targeted, which regulates a two-component system of bacterial pathogenesis, and initiates DNA replication and cell division. In the current study a computational approach have been described for drug development against C. diphtheriae infections by inhibiting MtrA protein by small molecules acting as potential inhibitors against it. Molecular docking analysis of the equilibrated MtrA protein revealed compound-0.2970, compound-0.3029, and compound-0.3016 from Asinex Library as the promising inhibitors based on their lowest binding energies (−9.8 kJ/mol, −9.2 kJ/mol, and −8.9 kJ/mol), highest gold scores (40.53, 47.41, and 48.41), drug-likeness and pharmacokinetic properties. The MD simulation studies of the identified top-ranked inhibitors at 100 ns elucidated the system stability and fluctuations in the binding pocket of MtrA protein. Molecular Dynamics Simulations of the top three docked complexes further revealed that the standard binding pocket was retained ensuring the system stability. The rearrangements of H-bonds, van der Waals, pi-pi, and solid hydrophobic interactions were also observed. The binding free energy calculations (MM/PBSA and MM/GBSA) suggested a fundamental binding capability of the ligand to the target receptor MtrA. Therefore, the current study has provided excellent candidates acting as potent inhibitors for developing therapeutic drugs against C. diphtheriae infections. However, in vivo and in vitro animal experiments and accurate clinical trials are needed to validate the potential inhibitory effect of these compounds.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Research on prediction of human oral bioavailability of drugs based on improved deep forest 基于改良深林的人体口服药物生物利用度预测研究。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-30 DOI: 10.1016/j.jmgm.2024.108851

{"title":"Research on prediction of human oral bioavailability of drugs based on improved deep forest","authors":"","doi":"10.1016/j.jmgm.2024.108851","DOIUrl":"10.1016/j.jmgm.2024.108851","url":null,"abstract":"<div>Human oral bioavailability is a crucial factor in drug discovery. In recent years, researchers have constructed a variety of different prediction models. However, given the limited size of human oral bioavailability data sets, the challenge of making accurate predictions with small sample sizes has become a critical issue in the field. The deep forest model, with its adaptively determinable number of cascade levels, can perform exceptionally well even on small-scale data. However, the original deep forest suffers unbalanced multi-grained scanning process and premature stopping of cascade forest training. In this paper, we propose a human oral bioavailability predict method based on an improved deep forest, called balanced multi-grained scanning mapping cascade forest (bgmc-forest). Firstly, the mordred descriptor method is selected to feature extraction, then enhanced features are obtained by the improved balanced multi-grained scanning, which solves the problem of missing features at both ends. And finally, the prediction results are obtained by feature mapping cascaded forests, which is based on principal component analysis and cascade forests, ensures the effectiveness of the cascade forest. The superiority of the model constructed in this paper is demonstrated through comparative experiments, while the effectiveness of the improved module is verified through ablation experiments. Finally the decision-making process of the model is explained by the shapley additive explanations interpretation algorithm.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Contrasting the effect of hinge region insertions and non-active site mutations on HIV protease-inhibitor interactions: Insights from altered flap dynamics 铰链区插入和非活性位点突变对 HIV 蛋白酶-抑制剂相互作用的影响对比：从改变的瓣膜动力学中获得启示。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-29 DOI: 10.1016/j.jmgm.2024.108850

{"title":"Contrasting the effect of hinge region insertions and non-active site mutations on HIV protease-inhibitor interactions: Insights from altered flap dynamics","authors":"","doi":"10.1016/j.jmgm.2024.108850","DOIUrl":"10.1016/j.jmgm.2024.108850","url":null,"abstract":"<div>HIV-1 protease (PR) enzyme is a viable antiretroviral drug target due to its crucial role in HIV maturation. Over many decades, the HIV-1 PR enzyme has exhibited mutations brought on by drug pressure and error-prone nature of HIV-1 reverse transcriptase. Non-active site mutations have played a pivotal role in drug resistance; however, their mechanism of action has not been fully elucidated. We investigated how non-active site mutations affect the conformational stability and drug binding ability of HIV-1 PR. In light of this, we studied a novel HIV-1 subtype C protease variant containing an insertion of valine (↑V) in the hinge region. We analysed the mutations in the presence and absence of ten background mutations. Molecular dynamics simulations revealed that both with and without the background mutations, the PR exhibited increased flexibility of hinge, flaps and fulcrum regions. This allowed the PR to adopt a wider flap conformation when in complex with several inhibitors. Additionally, the simulations revealed that the protease inhibitors (PIs) could not bring the mutated variant proteases into a stable, closed conformation, resulting in increased solvent exposure of the inhibitors. Together, these results suggest that the mutations decrease the favourability of binding by altering the dynamics of the flap regions. Notably, the insertion mutation increased PR hinge flexibility and the introduction of background mutations compensated for this by stabilising the cantilever and hinge regions. Together, these findings provide insight into how non-active site mutations affect PR conformational dynamics in critical areas of the PR thus impacting on drug binding capacity and potentially contributing to drug resistance.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1093326324001505/pdfft?md5=a95ddd1453ef958468a5ebe54b57258a&pid=1-s2.0-S1093326324001505-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Immunoinformatic approach for multi-epitope vaccine design against Staphylococcus aureus based on hemolysin proteins 基于溶血素蛋白的多表位金黄色葡萄球菌疫苗设计的免疫形式化方法。

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-23 DOI: 10.1016/j.jmgm.2024.108848

{"title":"Immunoinformatic approach for multi-epitope vaccine design against Staphylococcus aureus based on hemolysin proteins","authors":"","doi":"10.1016/j.jmgm.2024.108848","DOIUrl":"10.1016/j.jmgm.2024.108848","url":null,"abstract":"<div>Staphylococcus aureus is a common bacterium that causes a variety of infections in humans. This microorganism produces several virulence factors, including hemolysins, which contribute to its disease-causing ability. The treatment of S. aureus infections typically involves the use of antibiotics. However, the emergence of antibiotic-resistant strains has become a major concern. Therefore, vaccination against S. aureus has gained attention as an alternative approach. Vaccination has the advantage of stimulating the immune system to produce specific antibodies that can neutralize bacteria and prevent infection. However, developing an effective vaccine against S. aureus has proven to be challenging. This study aimed to use in silico methods to design a multi-epitope vaccine against S. aureus infection based on hemolysin proteins. The designed vaccine contained four B-cell epitopes, four CTL epitopes, and four HTL epitopes, as well as the ribosomal protein L7/L12 and pan-HLA DR-binding epitope, included as adjuvants. Furthermore, the vaccine was non-allergenic and non-toxic with the potential to stimulate the TLR2-, TLR-4, and TLR-6 receptors. The predicted vaccine exhibited a high degree of antigenicity and stability, suggesting potential for further development as a viable vaccine candidate. The population coverage of the vaccine was 94.4 %, indicating potential widespread protection against S. aureus. Overall, these findings provide valuable insights into the design of an effective multi-epitope vaccine against S. aureus infection and pave the way for future experimental validations.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142055870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

First-principles study of electrochemical H2O2 production on Pd-B40 single-atom catalyst 在 Pd-B40 单原子催化剂上电化学生产 H2O2 的第一性原理研究

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-13 DOI: 10.1016/j.jmgm.2024.108847

{"title":"First-principles study of electrochemical H2O2 production on Pd-B40 single-atom catalyst","authors":"","doi":"10.1016/j.jmgm.2024.108847","DOIUrl":"10.1016/j.jmgm.2024.108847","url":null,"abstract":"<div>Hydrogen peroxide (H2O2), a versatile green compound, is increasingly in demand. The electrochemical two-electron oxygen reduction reaction (2e− ORR) is a simple and environmentally friendly substitute method to the traditional anthraquinone oxidation method for H2O2 production. This study systematically investigates the 2e− ORR process on single transition metal atom-loaded boron fullerene (M − B40) using density functional theory calculations. In evaluating the stability of the catalysts, we found that Au, Pd, Pt, Rh, and Ir atoms adsorbed on hexagonal or heptagonal sites of B40 exhibit good stability. Among these, Pd-modified B40 heptagonal cavity (Pd-B40-heptagonal) demonstrates an ideal Gibbs free energy change for OOH* (4.49 eV) and efficiently catalyzes H2O2 production at a low overpotential (0.27 V). Electronic structure analysis reveals that electron transfer between Pd-B40-heptagonal and adsorbed O2 facilitates O2 activation. Additionally, the high 2e− ORR activity of Pd-B40-heptagonal is attributed to electron transfer from the Pd-d orbitals to the π* anti-bonding of p orbitals of OOH*, moderately activating the O-O bond. This study offers valuable understanding designing high-performance electrocatalysts for 2e− ORR.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142006742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The potential of Chlorella spp. as antiviral source against African swine fever virus through a virtual screening pipeline 通过虚拟筛选管道研究小球藻作为非洲猪瘟病毒抗病毒源的潜力

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-10 DOI: 10.1016/j.jmgm.2024.108846

{"title":"The potential of Chlorella spp. as antiviral source against African swine fever virus through a virtual screening pipeline","authors":"","doi":"10.1016/j.jmgm.2024.108846","DOIUrl":"10.1016/j.jmgm.2024.108846","url":null,"abstract":"<div>African swine fever (ASF) causes high mortality in pigs and threatens global swine production. There is still a lack of therapeutics available, with two vaccines under scrutiny and no approved small-molecule drugs. Eleven (11) viral proteins were used to identify potential antivirals in in silico screening of secondary metabolites (127) from Chlorella spp. The metabolites were screened for affinity and binding selectivity. High-scoring compounds were assessed through in silico ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) predictions, compared to structurally similar drugs, and checked for off-target docking with prepared swine receptors. Molecular dynamics (MD) simulations determined binding stability while binding energy was measured in Molecular Mechanics - Generalized Born Surface Area (MMGBSA) or Poisson-Boltzmann Surface Area (MMPBSA). Only six (6) compounds passed until MD analyses, of which five (5) were stable after 100 ns of MD runs. Of these five compounds, only three had binding affinities that were comparable to or stronger than controls. Specifically, phytosterols 24,25-dihydrolanosterol and CID 4206521 that interact with the RNA capping enzyme (pNP868R), and ergosterol which bound to the Erv-like thioreductase (pB119L). The compounds identified in this study can be used as a theoretical basis for in vitro screening to develop potent antiviral drugs against ASFV.</div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hex-star phosphorene nanosheets as sequencing material for DNA/RNA strands – A first-principles investigation 作为 DNA/RNA 链测序材料的六芒星磷烯纳米片--第一原理研究

IF 2.7 4区生物学

Journal of molecular graphics & modelling Pub Date : 2024-08-09 DOI: 10.1016/j.jmgm.2024.108845

引用次数: 0