Journal of molecular graphics & modelling最新文献

{"title":"DeepTree-AAPred: Binary tree-based deep learning model for anti-angiogenic peptides prediction","authors":"Fan Zhang,&nbsp;Jinfeng Li,&nbsp;Chun Fang","doi":"10.1016/j.jmgm.2025.108982","DOIUrl":"10.1016/j.jmgm.2025.108982","url":null,"abstract":"<div><div>Anti-angiogenic peptides (AAPs) show important potential in tumor therapy by limiting the growth and metastasis of tumor cells. Accurate prediction of AAPs is of very positive significance for the therapeutic efficacy of tumors. The high cost of wet experiments limits the application of large-scale screening. Existing computational methods, although able to solve the problem of wet experiments, still lack in performance. To this end, a deep learning-based anti-angiogenic peptide prediction model, DeepTree-AAPred, is proposed in this study. The model utilizes a binary tree structure and employs protein language pre-training models ProtBERT and ESM-2 to extract 1D and 2D generalized features. It further captures local features and contextual dependencies using BiLSTM and TextCNN, ultimately fusing the output features for AAPs prediction. Extensive experimental results on standard datasets show that DeepTree-AAPred outperforms existing computational methods, demonstrating its potential for practical application in AAPs tasks.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108982"},"PeriodicalIF":2.7,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510109","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}

{"title":"DFT investigation of geometrical, vibrational, elastic, electronic, optical, and thermoelectric properties of aluminum pnictogens compounds","authors":"Pankaj Kumar ,&nbsp;Debesh R. Roy","doi":"10.1016/j.jmgm.2025.108995","DOIUrl":"10.1016/j.jmgm.2025.108995","url":null,"abstract":"<div><div>The aim of this study is to investigate the geometrical, vibrational, elastic, electronic, optical, and thermoelectric characteristics of aluminum pnictides in monolayer square lattice and bilayer hexagonal phases (<em>s</em>- and <em>h</em>-AlX; X = N, P, As) using first principles. The <em>s</em>- and <em>h</em>-AlX materials are mechanically, energetically, and dynamically stable, through phonon dispersion and elastic properties investigations. It was observed that <em>s</em>-AlX materials exhibited both direct and indirect bandgaps, whereas <em>h</em>-AlX materials exhibited indirect bandgap behavior. The energy bandgap values for <em>s</em>- and <em>h</em>-AlX materials measured between 0.79 eV and 3.49 eV for the PBE functional, and between 1.49 eV and 4.74 eV for the HSE06 functional. The effective mass, mobility and relaxation time of electron carriers as well as hole carriers from the band structure of <em>s</em>- and <em>h</em>-AlX are examined to gain a better perception into these materials. The AlP monolayer square lattice phase has the highest mobility and relaxation time of 266129.60 cm²V⁻¹s⁻¹ and 740369.83 fs among entire <em>s</em>- and <em>h</em>-AlX materials. The optical characteristics of <em>s</em>- and <em>h</em>-AlX materials are examined in the existence of field polarizations. The thermoelectric properties of the AlX materials are assessed for temperature dependent. Our investigated results expose that AlP/AlP and AlAs/AlAs are the proficient thermoelectric materials at room temperature in the considered sequence. The present investigation shows that the <em>s</em>- and <em>h</em>-AlX materials are mostly active in the UV region of electromagnetic spectrum, and may find applications in UV-photodetectors and UV-protectant materials.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108995"},"PeriodicalIF":2.7,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143529670","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}

{"title":"Fragment-level feature fusion method using retrosynthetic fragmentation algorithm for molecular property prediction","authors":"Qifeng Jia ,&nbsp;Yekang Zhang ,&nbsp;Yihan Wang ,&nbsp;Tiantian Ruan ,&nbsp;Min Yao ,&nbsp;Li Wang","doi":"10.1016/j.jmgm.2025.108985","DOIUrl":"10.1016/j.jmgm.2025.108985","url":null,"abstract":"<div><div>Recent advancements in Artificial Intelligence (AI) and deep learning have had a significant impact on drug discovery. The prediction of molecular properties, such as toxicity and blood-brain barrier (BBB) permeability, is crucial for accelerating drug development. The accuracy of these predictions largely depends on the selection of molecular descriptors. Self-supervised learning (SSL) has gained prominence due to its strong generalization capabilities. Graph contrastive learning (GCL), a type of SSL, is particularly useful in this context. Current GCL methods for molecular graphs use various data augmentation techniques, which may potentially alter the inherent structure of molecules. Additionally, traditional single-perspective representations do not fully capture the complexity of molecules. We present RFA-FFM (Fragment-level Feature Fusion Method using Retrosynthetic Fragmentation Algorithm), which integrates molecular representations from multiple perspectives. This method employs two strategies: (1) contrasting chemical information from fragments generated by two retrosynthetic methods to provide detailed contrastive insights; (2) fusing chemical information at different levels of molecular hierarchy, including the entire molecule and its fragments. Experiments show that RFA-FFM enhances the performance of deep learning models in predicting molecular properties, improving ROC-AUC scores by 0.3 %–2.6 % compared to baselines across four classification benchmarks. Case studies on hepatitis B virus datasets demonstrate that RFA-FFM outperforms baselines by 7 %–11 %. When compared to BPE and CC-Single fragmentation algorithms, RFA-FFM shows a 2 %–4 % improvement in BBB permeability tasks, thus demonstrating its effectiveness in predicting molecular properties.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108985"},"PeriodicalIF":2.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143487032","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}

{"title":"Exploring the structural and functional dynamics of trimeric and tetrameric states of influenza encoded PB1-F2 viroporin through molecular dynamics simulations","authors":"Sehrish Jamal ,&nbsp;Syed Tarique Moin ,&nbsp;Shozeb Haider","doi":"10.1016/j.jmgm.2025.108983","DOIUrl":"10.1016/j.jmgm.2025.108983","url":null,"abstract":"<div><div>Influenza Viruses have always been a major health concern due to their highly contagious nature. The PB1-F2 viroporin encoded by the influenza A virus is known to be a pro-apoptotic protein involved in cell death induction of the host immune cells. The structural arrangement and the mode of action of PB1-F2 viroporin have not been fully understood yet. Nonetheless, there is limited information on the oligomeric state of PB1-F2 and its possible role in the pore formation which could act as a channel for ion transport. The probable oligomeric structural existences of the viroporin and their channel-like behavior need to be explored in light of experimental reports cited in the literature. In our study, we report on the structural and dynamical properties of the trimeric and tetrameric state of PB1-F2, investigated by molecular dynamics simulations with improved sampling of conformational states as the initial focus of the study is to establish a rationale for their existence in a lipid environment. The simulation study provides detailed information on the mitochondrial membrane permeation pathway which causes the leakage of mitochondrial contents like cytochrome C and induces apoptosis. By focusing on low-order oligomers, trimer, and tetramer, we have identified key pore-forming characteristics that serve as a foundation for understanding the pro-apoptotic activity of PB1-F2. The structural and dynamical properties of these states were evaluated in the light of experimental reports, which reveal the tetrameric form to be the preferable state in the lipid environment, demonstrating superior structural stability, effective channel symmetry, and ion permeation compared to the higher-order oligomers besides trimer including pentameric and hexameric assemblies. The simulation results also explore the typical ion transportation criteria based on finding a less energetic barrier for ions/water molecules crossing the membrane.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108983"},"PeriodicalIF":2.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143510110","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}

{"title":"Targeting GPR52 for potential agonists for schizophrenia therapy: A computational drug discovery study","authors":"Selinay Demir,&nbsp;Güzin Tunca Alparslan","doi":"10.1016/j.jmgm.2025.108994","DOIUrl":"10.1016/j.jmgm.2025.108994","url":null,"abstract":"<div><div>G Protein-Coupled Receptors (GPCRs) are one of the most attractive therapeutic targets due to their active role in different systems and disease types. The increasing three-dimensional structure information of GPCRs has made them interesting for Structure-Based Drug Design (SBDD) studies. There are various orphan GPCRs whose endogenous molecules have not yet been identified, although their structural information is known. The recent discovery of the three-dimensional structure of GPR52, an orphan GPCR involved in central nervous system diseases, made it stand out as a drug target. In this study, it is aimed to find a lead drug molecule candidate for GPR52 by using structure-based drug design techniques. The study comprises a set of SBDD methods, including preparation of a small molecule library, pharmacophore modeling, molecular docking, consensus scoring, molecular dynamics simulations, calculation of binding free energy, and <em>in silico</em> pharmacokinetic studies for GPR52. It is expected that the molecules obtained as a result of the study may be strong candidates for <em>in vitro</em> and <em>in vivo</em> experiments or could be used as lead drug molecules in new drug discovery and development studies.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108994"},"PeriodicalIF":2.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143519351","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}

{"title":"COVID-19 detection via isobutyric acid biomarker: A DFT computational study on beryllium-doped C60 fullerene","authors":"Stève-Jonathan Koyambo-Konzapa ,&nbsp;Ali Oubella ,&nbsp;Ali Altharawi ,&nbsp;Taibah Aldakhil","doi":"10.1016/j.jmgm.2025.108987","DOIUrl":"10.1016/j.jmgm.2025.108987","url":null,"abstract":"<div><div>The COVID-19 pandemic has underscored the urgent need for rapid, accurate, and non-invasive diagnostic methods. This study explores the potential of beryllium-doped C₆₀ fullerene as a sensor for detecting COVID-19 via isobutyric acid (ISO-But), a biomarker found in the breath of infected individuals. By employing Density Functional Theory (DFT), we analyze the electronic and structural properties of pristine and metal-doped C60 fullerenes (Beryllium (Be) and Calcium (Ca)), focusing on their interactions with isobutyric acid. Our findings reveal that BeC₅₉, combined with isobutyric acid, displays a colorimetric response within the visible spectrum, indicating its suitability for point-of-care diagnostics. With rapid recovery and strong interaction properties, this sensor design promises to advance non-invasive COVID-19 detection, making it accessible and feasible for real-time applications.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108987"},"PeriodicalIF":2.7,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143465025","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}

{"title":"Drug likeliness, pharmacokinetics profiling and efficacy of Polyscias fulva bioactive compounds in the management of uterine fibroids; An integrative in silico and in vivo approach","authors":"Kenedy Kiyimba ,&nbsp;Lincoln Munyendo ,&nbsp;Samuel Baker Obakiro ,&nbsp;Yahaya Gavamukulya ,&nbsp;Ayaz Ahmed ,&nbsp;Mohammed Iqbal Choudhary ,&nbsp;Muhammad Shafiq ,&nbsp;Zaheer Ul-Haq ,&nbsp;Eric Guantai","doi":"10.1016/j.jmgm.2025.108984","DOIUrl":"10.1016/j.jmgm.2025.108984","url":null,"abstract":"<div><div><em>Polyscias fulva</em> is traditionally used in Uganda for the management of Uterine fibroids (UF). However, there is paucity of data regarding its efficacy, biological targets and potential mechanisms of action hence prompting scientific validation process through insilico and invivo approaches. In this study, we utilized network pharmacology, molecular docking, molecular dynamic simulations and invivo assays to investigate the drug likeliness, pharmacokinetics and efficacy of <em>Polyscias fulva</em> against Uterine fibroids.</div><div>Four <em>Polyscias fulva</em> bioactive compounds; pinoresinol, lichexanthone, methyl atarate, β-sitosterol exhibited drug likeness properties with moderate safety profiles. Forty-eight (48) uterine fibroid targets were identified as potential targets for the eleven <em>Polyscias fulva compounds</em>. Protein-protein interaction (PPI) analysis revealed four key targets (HIF1A, ESR1, EGFR, and CASP3). The KEGG pathway and GO enrichment analyses revealed that these key targets play significant roles in regulating the positive regulation of cyclin-dependent protein serine/threonine kinase activity, positive regulation of nitric-oxide synthase activity and positive regulation of transcription, DNA-templated. β-sitosterol demonstrated the strongest binding affinity with the four targets, showing particularly strong affinities for EGFR (−9.75 kcal/mol) and HIF1A (−9.21 kcal/mol). Molecular dynamics (MD) simulations revealed high stability in these protein-ligand complexes, with CASP3 displaying the lowest deviation and most consistent RMSD (0.14 nm) of the protein, followed by EGFR (0.25), HIF1A (0.29), and ESR1 (0.79). In-vivo evaluation on female Wistar rats with <em>Polyscias fulva</em> ethanolic extract showed an ameliorative effect of the extracts against monosodium glutamate-induced (MSG) UF. Treated animals exhibited a decrease in serum proteins, cholesterol, estrogen, and progesterone levels (P &lt; 0.05) and the extract preserved uterine tissue histoachitecture as compared to controls. In conclusion, <em>Polyscias fulva</em> demonstrates potential ameliorative activity against UF with promising pharmacokinetic properties and safety profiles.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108984"},"PeriodicalIF":2.7,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143487077","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}

{"title":"Charge transfer and photophysical properties of DSSCs based on different π-conjugated bridges: DFT and TD-DFT study","authors":"Yi Yang ,&nbsp;Xin Miao ,&nbsp;Chuanlong Liu ,&nbsp;Yuwen Huang ,&nbsp;Linhan Li ,&nbsp;Lingpeng Zeng ,&nbsp;Jiajun Li ,&nbsp;Heyang Sun ,&nbsp;Mingjianshuo Gong","doi":"10.1016/j.jmgm.2025.108986","DOIUrl":"10.1016/j.jmgm.2025.108986","url":null,"abstract":"<div><div>Dye-sensitized solar cells (DSSCs) are photovoltaic devices that directly convert solar radiation into current, in which the dye sensitizer serves as a critical structure that plays a significant role in determining the performance and conversion efficiency of DSSCs devices. In this paper, a series of D-A-π-A type dyes are designed, in which 2,2′-bithiophene, 1,1′-biphenyl as well as C=C and azo groups are used as π-conjugated bridges to transport electrons, respectively. The ground and excited state properties of several molecules were analyzed by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The results show that the thiophene-based π-bridges have smaller frontier molecular orbital energy gaps and more red-shifted UV–vis absorption peaks, which are mainly attributed to the higher electron cloud density in the thiophene ring. At the same time, the addition of azo groups could further redshift the absorption peaks, mainly due to the existence of a large number of π-electrons in the azo bonds, which can reduce the energy required for electron transitions. In addition, it is also equally concluded that better photophysical properties are obtained by combining π-bridges of thiophenes with azo groups by means of transition density matrix, chemical reactivity parameters, photovoltaic parameter calculations and so on.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"137 ","pages":"Article 108986"},"PeriodicalIF":2.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445552","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}

{"title":"Molecular modelling of 6-oxo-5-Sulfanyl-1H-Pyridine-3-Carboxylic acid and its adsorption with the silver complex: Structural, optical, charge transference, dynamics and docking to nipah virus","authors":"R. Sravanthi ,&nbsp;S. Mahalakshmi ,&nbsp;Jayavelu Udaya Prakash ,&nbsp;S. Sakthivel","doi":"10.1016/j.jmgm.2025.108978","DOIUrl":"10.1016/j.jmgm.2025.108978","url":null,"abstract":"<div><div>This investigation employs DFT to evaluate the structural, molecular, and electronic feature variations of 6-oxo-5-sulfanyl-1H-pyridine-3-carboxylic acid in gas alongside various solvent media. The complex interactions occurring within the molecule are recognised using the Independent gradient model. The application of various electric fields are used to determine the electrical properties of the compound. The topographical inspection shows extreme electron-dense zones to display a good electron reception character of the molecule. The intense covalence nature is maximal between the aromatic zone's C-C and C-N regions. The compound possesses a maximum interaction with the (LP) → π∗ and π → π∗ transitions. The optical and absorbance property shows an upright enhancement in the addition of the solvents. The significant transference of charges inside the compound is signified using the D and H index values and heat maps. The thermal assessment established that the compound is sustainable at varied temperatures with the pressure at 1 atm. The carboxylate ion of 6O5S1HP3CA interacts with the Ag + clusters and its adsorption characteristics are confirmed by the SERS spectrum. The complex's stability is determined by the MD simulations at various speeds. The physiological scrutiny demonstrates that both the compound and complex are benign and the antiviral activities were studied for Nipah virus for the proteins 7pno and 7skt.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"136 ","pages":"Article 108978"},"PeriodicalIF":2.7,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143430176","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}

{"title":"Supercapacitor Materials Database Generated using Web Scrapping and Natural Language Processing","authors":"Tikam C. Soni ,&nbsp;M.K. Manoj ,&nbsp;M.L. Verma ,&nbsp;Manwendra. K. Tripathi","doi":"10.1016/j.jmgm.2025.108980","DOIUrl":"10.1016/j.jmgm.2025.108980","url":null,"abstract":"<div><div>Electrochemical energy storage plays a vital role in achieving environmental sustainability. Supercapacitors emerge as promising alternatives to batteries due to their high-power density and extended lifespan. Extensive scholarly research has been conducted on supercapacitor energy storage, providing valuable insights into materials and performance parameters. This study presents a comprehensive supercapacitor materials database, created by web scraping the article abstracts from the Scopus database and processing them using Regular Expressions, the BatteryBERT Language Model, and the ChemDataExtractor Python package. The final database comprises 28,269 recorded entries across 21 relevant fields, including metadata, electrode and electrolyte materials, and seven key device performance parameters. This initiative aims to establish a novel database that can support the prediction and design of advanced supercapacitors.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"136 ","pages":"Article 108980"},"PeriodicalIF":2.7,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143430175","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}