Journal of Biomolecular Structure & Dynamics最新文献

{"title":"Antipyretic effects of Xiangqin Jiere granules on febrile young rats revealed by combining pharmacodynamics, metabolomics, network pharmacology, molecular biology experiments and molecular docking strategies.","authors":"Xiying He, Jieqiong Cui, Huayan Li, Yang Zhou, Xinchen Wu, Chunrong Jiang, Zhichang Xu, Ruirui Wang, Lei Xiong","doi":"10.1080/07391102.2024.2301761","DOIUrl":"10.1080/07391102.2024.2301761","url":null,"abstract":"<p><p>Xiangqin Jiere granules (XQJRG) is a proprietary Chinese medicine treating children's colds and fevers, but its mechanism of action is unclear. The aim of this study was to explore the antipyretic mechanisms of XQJRG based on pharmacodynamics, non-targeted metabolomics, network pharmacology, molecular biology experiments, molecular docking, and molecular dynamics (MD) simulation. Firstly, the yeast-induced fever model was constructed in young rats to study antipyretic effect of XQJRG. Metabolomics and network pharmacology studies were performed to identify the key compounds, targets and pathways involved in the antipyretic of XQJRG. Subsequently, MetScape was used to jointly analyze targets from network pharmacology and metabolites from metabolomics. Finally, the key targets were validated by enzyme-linked immunosorbent assay (ELISA), and the affinity and stability of key ingredient and targets were evaluated by molecular docking and MD simulation. The animal experimental results showed that after XQJRG treatment, body temperature of febrile rats was significantly reduced, 13 metabolites were significantly modulated, and pathways of differential metabolite enrichment were mainly related to amino acid and lipid metabolism. Network pharmacology results indicated that quercetin and kaempferol were the key active components of XQJRG, <i>TNF</i>, <i>AKT1</i>, <i>IL6</i>, <i>IL1B</i> and <i>PTGS2</i> were core targets. ELISA confirmed that XQJRG significantly reduced the plasma concentrations of IL-1β, IL-6, and TNF-α, and the hypothalamic concentrations of COX-2 and PGE2. Molecular docking demonstrated that the binding energies of kaempferol to the core targets were all below -5.0 kcal/mol. MD simulation results showed that the binding free energies of TNF-kaempferol, IL6-kaempferol, IL1B-kaempferol and PTGS2-kaempferol were -87.86 kcal/mol, -70.41 kcal/mol, -69.95 kcal/mol and -106.67 kcal/mol, respectively. In conclusion, XQJRG has antipyretic effects on yeast-induced fever in young rats, and its antipyretic mechanisms may be related to the inhibition of peripheral pyrogenic cytokines release by constituents such as kaempferol, the reduction of hypothalamic fever mediator production, and the amelioration of disturbances in amino acid and lipid metabolism.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4183-4200"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of hematopoietic progenitor kinase 1 inhibitors using machine learning-based screening and free energy perturbation.","authors":"Dazhi Feng, Bo Liu, Zhiwei Chen, Jinyi Xu, Meiyu Geng, Wenhu Duan, Jing Ai, Hefeng Zhang","doi":"10.1080/07391102.2024.2301754","DOIUrl":"10.1080/07391102.2024.2301754","url":null,"abstract":"<p><p>Hematopoietic progenitor kinase 1 (HPK1) is a key negative regulator of T-cell receptor (TCR) signaling and a promising target for cancer immunotherapy. The development of novel HPK1 inhibitors is challenging yet promising. In this study, we used a combination of machine learning (ML)-based virtual screening and free energy perturbation (FEP) calculations to identify novel HPK1 inhibitors. ML-based screening yielded 10 potent HPK1 inhibitors (IC₅₀ < 1 μM). The FEP-guided modification of the in-house false-positive hit, <b>DW21302</b>, revealed that a single key atom change could trigger activity cliffs. The resulting <b>DW21302-A</b> was a potent HPK1 inhibitor (IC₅₀ = 2.1 nM) and potently inhibited cellular HPK1 signaling and enhanced T-cell function. Molecular dynamics (MD) simulations and ADME predictions confirmed <b>DW21302-A</b> as candidate compound. This study provides new strategies and chemical scaffolds for HPK1 inhibitor development.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4152-4164"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the potential of <i>Psidium guajava</i> derived phytoconstituents as anticholinesterase inhibitor to combat Alzheimer's disease: an <i>in-silico</i> and <i>in-vitro</i> approach.","authors":"Kunal Bhattacharya, Atanu Bhattacharjee, Manodeep Chakraborty","doi":"10.1080/07391102.2024.2301930","DOIUrl":"10.1080/07391102.2024.2301930","url":null,"abstract":"<p><p>Acetylcholinesterase (AChE) inhibitors play a crucial role in the treatment of Alzheimer's disease. These drugs increase acetylcholine levels by inhibiting the enzyme responsible for its degradation, which is a vital neurotransmitter involved in memory and cognition. This intervention intermittently improves cognitive symptoms and augments neurotransmission. This study investigates the potential of <i>Psidium guajava</i> fruit extract as an acetylcholinesterase (AChE) inhibitor for Alzheimer's disease treatment. Molecular characteristics and drug-likeness were analyzed after HR-LCMS revealed phytocompounds in an ethanolic extract of <i>Psidium guajava</i> fruit. Selected phytocompounds were subjected to molecular docking against AChE, with the best-docked compound then undergoing MD simulation, MMGBSA, DCCM, FEL, and PCA investigations to evaluate the complex stability. The hit compound's potential toxicity and further pharmacokinetic features were also predicted. Anticholinesterase activity was also studied using <i>in vitro</i> assay. The HR-LCMS uncovered 68 compounds. Based on computational analysis, Fluspirilene was determined to have the highest potential to inhibit AChE. It was discovered that the Fluspirilene-AChE complex is stable and that Fluspirilene has a high binding affinity for AChE. Extract of <i>Psidium guajava</i> fruit significantly inhibits AChE (88.37% at 200 μg/ml). It is comparable to the standard AChE inhibitor Galantamine. Fluspirilene exhibited remarkable binding to AChE. <i>Psidium guajava</i> fruit extract demonstrated substantial AChE inhibitory activity, indicating its potential for Alzheimer's treatment. The study underscores natural sources' significance in drug discovery.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4240-4257"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A phenanthroline-based erbium (III) complex: molecular docking, DNA/BSA -binding and biological evaluation.","authors":"Faisal F Albaqami, Ameer S Sahib, Khalid M Alharthy, Ali Altharawi, Mohammad Y Alshahrani, Mohammed Abed Jawad, Muath Suliman, Irfan Ahmad","doi":"10.1080/07391102.2023.2300130","DOIUrl":"10.1080/07391102.2023.2300130","url":null,"abstract":"<p><p>With the help of both theoretical as well as experimental research, <i>in vitro</i> binding research with CT-DNA (calf thymus) and BSA (bovine serum albumin) were carefully examined to figure out the chemotherapeutic and pharmacokinetic facets of the Erbium complex, which contains 1,10-phenanthroline (Phen). The binding characteristics and the mechanism of complex's interaction with DNA as well as the protein were determined utilizing fluorescence quenching method. Findings indicated that the complex's interaction with DNA <i>via</i> groove binding into DNA's minor grooves, with their binding constants falling within the 10⁴ M^-1 range. Furthermore, thermodynamic characteristics and the fluorescence emission of the tryptophan residues of the protein were obtained through fluorescence quenching studies at different temperatures. According to the results of the binding constants, the protein's interactions with the Er- complex were moderate, demonstrating that the compound may be transported effectively by the protein. Molecular docking results supported that of the experimental research. The HeLa and MCF-7 cancer cell lines, along with the normal human fibroblast cell line, were used in an MTT assay evaluation of the Er-complex cytotoxicity. The Er-complex displayed a selective inhibitory effect on the proliferation of different cancer cells.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3873-3885"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, molecular docking, and molecular dynamic simulation studies of new 1,3,4-thiadiazole derivatives as potential apoptosis inducers in A549 lung cancer cell line.","authors":"Leyla Yurttaş, Asaf Evrim Evren, Huda AlChaib, Halide Edip Temel, Gülşen Akalin Çiftçi","doi":"10.1080/07391102.2023.2300125","DOIUrl":"10.1080/07391102.2023.2300125","url":null,"abstract":"<p><p>1,3,4-Thiadiazoles are structures that are bioisosteres of 1,3,4-oxadiazole and pyrimidine ring, which are found in the structure of many drugs and anticancer active newly studied derivatives. In the past, high effect profiles have been observed in many molecules created, based on the anticancer effects of the 2-amino-1,3,4-thiadiazole (NSC 4728) molecule and acetazolamide molecules. Focusing on these molecules and evaluating them in terms of mechanistic effects, twelve new <i>N</i>-[5-((3,5-dichlorophenoxy) methyl]-1,3,4-thiadiazole derivatives (<b>3a-3i</b>) were synthesized and their biological activities were investigated in lung cancer cells. The anticancer effects of the compounds were evaluated on the A549 and L929 cell lines. Compound <b>3f</b>, namely 2-[(5-chlorobenzotiyazol-2-yl)thio]-<i>N</i>-[5-[(3,5-dichlorophenoxy)methyl]-1,3,4-thiadiazol-2-yl]acetamide, showed better activity than cisplatin, exhibiting high inhibitory potency (IC₅₀: <0.98 μg/mL) and selectivity against A549 cell line even at the lowest concentration tested. Compounds <b>3c</b>, <b>3f</b>, and <b>3h</b> with the lowest IC₅₀ values of the compounds exhibited an excellent percentage of apoptosis between 72.48 and 91.95% compared to cisplatin. The caspase-3 activation and mitochondrial membrane potential change of the aforementioned three compounds were also studied. Moreover, matrix metalloproteinase-9 (MMP-9) inhibition potential of all final compounds was also investigated and IC₅₀ values for compounds <b>3b</b> and <b>3g</b> were identified as 154.23 and 107.28 µM. Molecular docking and molecular dynamic simulation studies for MMP-9 enzyme inhibition were realized on these compounds and the nitrogen atoms of amide and thiadiazole moieties' ascertained that they play a key role in chelating with Zn metal, at the same time, (thio)ether moieties allow conformational change resulting in the ligand can make more stable contacts.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3814-3829"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139080588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into the conformational, secondary structural, dynamical and hydration pattern changes of glucose mediated glycated HSA: a molecular dynamics approach.","authors":"Jayanth Jeevanandam, N Arul Murugan, N T Saraswathi","doi":"10.1080/07391102.2024.2301749","DOIUrl":"10.1080/07391102.2024.2301749","url":null,"abstract":"<p><p>The robust structural nature of human serum albumin (HSA) is responsible for its multifarious functional property. The site specific glycation of HSA due to hyperglycaemia (excess glucose) causes structural changes which have an impact on the functioning of the protein. This work investigates the effects of glucose-mediated glycation in the altered inter-domain motion, distorted binding site conformation and modified hydration patterns, Trp214 orientation, and secondary structure transition using simulation approach. Here we have observed an increase of turns in the helices of glycated HSA, which modulates the open-close conformation of Sudlow I & II. The secondary structure changes of glycated HSA indicate plausible reduction in the alpha helical content in the helices which participates in ligand binding. It also affects geometrical features of drug binding sites (Sudlow I and II) such as volume and hydration. We found that glycation disturbs domain specific mobility patterns of HSA, a substantial feature for albumin drug binding ability which is also correlated with changes in the local environment of Trp214.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4125-4137"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139424820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pharmaceutical manifestation of Knoevenagel condensed metal (II) complexes through virtual, <i>in vitro</i> and <i>in vivo</i> assessments.","authors":"Samuel Michael, Porkodi Jeyaraman, Bhuvaneswari Marimuthu, Rajasekar Rajamanikam, Radha Thanasamy, Karuppiah Arunsunai Kumar, Liviu Mitu, Natarajan Raman","doi":"10.1080/07391102.2023.2301059","DOIUrl":"10.1080/07391102.2023.2301059","url":null,"abstract":"<p><p>Sulphur containing compounds possess a great deal of interest due to wide range of beneficial activities towards biotic species. This work also deals with the study of biological examination of newly synthesized sulphur containing Cu(II) and Zn(II) complexes derived from (E)-4-(phenylimino)-3-((E)-1-(phenylimino)ethyl)pent-2-ene-1-thiol Schiff bases. Moreover, the DNA nuclease efficiency of the synthesized metal complexes is studied by UV absorption studies, Fluorescence studies, Viscosity and CV titrations which confirm the intercalative mode of binding. Pharmacokinetic studies and drug like activity of these compounds are screened with the help of SWISS ADME online freeware. Their morphological nature is corroborated by various spectral techniques. Optimized geometry and biologically accessible nature of the synthesized compounds are investigated by Gaussian 09 W software. Interestingly, molecular docking studies are carried out against cancer DNA and 6J10 cancer cell. Anti-inflammatory and <i>in vitro</i> antioxidant activities have been studied to validate the theoretical prediction. Based on these preliminary pharmacological activities, the <i>in vitro</i> cytotoxicity and <i>in vivo</i> antitumor activities are examined using MCF-7, HeLa, Hep-2, HepG-2 and Ehrlich ascites carcinoma (EAC) cell lines. All the above examinations reveal that the nitro substituted transition metal complexes possess higher biological bustle.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4028-4042"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational exploration of allosteric inhibitors targeting CDK4/CDK6 proteins: a promising approach for multi-target drug development.","authors":"Mahmood Khan, Kamaljot Singh, Sara Khan, Basharat Ahmad, Aneela Khushal, Sun Yingning","doi":"10.1080/07391102.2023.2300121","DOIUrl":"10.1080/07391102.2023.2300121","url":null,"abstract":"<p><p>Cyclin-dependent kinases (CDKs) play a pivotal role in orchestrating the intricate regulation of the cell cycle, a fundamental process governing cell growth and division. In particular, CDK4 and CDK6 are critical for the transition from the G1 phase to the S phase, where Deoxyribonucleic acid (DNA) replication occurs, and their dysregulation is linked to various diseases, notably cancer. While ATP-binding site inhibitors for CDKs are well-documented, this study focuses on uncovering allosteric inhibitors, providing a fresh perspective on CDK inhibition. Computational techniques were employed in this investigation, utilizing Molecular Operating Environment (MOE) for virtual screening of a drug-like compound library. Moreover, the stability of the most promising binding inhibitors was assessed through Molecular Dynamics (MD) simulations and MMPBSA/MMGBSA analyses. The outcome reveals that three inhibitors (C1, C2, and C3) exhibited the strongest binding affinity for CDK4/CDK6, as corroborated by docking and simulation analyses. The computed binding energies ranged from -6.1 to -7.6 kcal/mol, underscoring the potency of these allosteric inhibitors. Notably, this study identifies key residues (PHE31, HIS95, HIS100, VAL101, ASP102, ASP104, and THR107) that play pivotal roles in mediating inhibitor binding within the allosteric sites. Among the findings, the C1-CDK4 complex and C2-CDK6 complex emerge as particularly promising inhibitors, exhibiting high binding energies, favorable interaction patterns, and sustained presence within the active site. This study contributes significantly to the pursuit of multi-target drugs against CDK4/CDK6 proteins, with potential implications for the development of innovative therapies across various disorders, including cancer and other cell cycle-related conditions.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"3783-3801"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139087030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In silico</i> and <i>in vitro</i> studies: investigating the chemical composition, DFT, molecular docking, and dynamic simulation of <i>Satureja candidissima (Munby) Briq</i> essential oil as a potential antibacterial agent.","authors":"Ainayat Ellah Saidi, Nebia Bouzidi, Mohammed Ziane, Mohammed Gherib, Chaimaa Rahila, Marius Mioc","doi":"10.1080/07391102.2024.2301742","DOIUrl":"10.1080/07391102.2024.2301742","url":null,"abstract":"<p><p>This study aimed to investigate the chemical composition and antibacterial properties of the essential oil (EO) derived from the aerial parts of <i>Satureja candidissima (Munby) Briq</i> (SC), as well as the mechanisms of interaction between SCEO chemical components and target proteins related to antibacterial activity mechanisms using a molecular docking approach, and for more accuracy molecular dynamic simulation and DFT calculations were carried out. The GC-MS technique was used to analyze the chemical composition of SCEO. The results showed that SCEO contained various chemical compounds, with pulegone being identified as the major component (53.26%). The results also indicated the presence of (+)-menthone (11.02%), borneol (4.43%), 2-cyclohexen-1-one, 3-methyl-6-(1-methylethylidene) (2.50%), and 3-octanol (2.09%). The study revealed that the SCEO displayed antibacterial activity against all tested gram-positive bacteria. To further understand the mechanism behind its antibacterial activity, <i>in silico</i> molecular docking studies were performed. The results indicated that the antibacterial effect of SCEO compounds could be due to the combination with enoyl-[acyl-carrier-protein] reductase [NADPH] FabI (PDB ID: 4ALL) in a variety of ways. The molecular dynamics simulation analysis yielded favorable outcomes for the docked complex involving 1<i>H</i>-cycloprop[e]azulen-7-ol, decahydro-1,1,7-trimethyl-4-methylene, and 1,4,7-tetramethyldecahydro-1<i>H</i>-cyclopropa[e]azulen-4-ol with enoyl-[acyl-carrier-protein] reductase [NADPH]. Geometry optimization, coupled with Density Functional Theory (DFT), can be employed to assess the importance of quantum chemical descriptors in elucidating potential antibacterial activity. Quantum descriptors were computed based on <i>E</i>_HOMO and <i>E</i>_LUMO. The results of this study provide important insights into the potential use of <i>Satureja candidissima (Munby) Briq</i> EO as antibacterial agent.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4043-4062"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139402995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GSLAlign: community detection and local PPI network alignment.","authors":"Umair Ayub, Hammad Naveed","doi":"10.1080/07391102.2024.2301757","DOIUrl":"10.1080/07391102.2024.2301757","url":null,"abstract":"<p><p>High throughput protein-protein interaction (PPI) profiling and computational techniques have resulted in generating a large amount of PPI network data. The study of PPI networks helps in understanding the biological processes of the proteins. The comparative study of the PPI networks helps in identifying the conserved interactions across the species. This article presents a novel local PPI network aligner 'GSLAlign' that consists of two stages. It first detects the communities from the PPI networks by applying the GraphSAGE algorithm using gene expression data. In the second stage, the detected communities are aligned using a community aligner that is based on protein sequence similarity. The community detection algorithm produces more separable and biologically accurate communities as compared to previous community detection algorithms. Moreover, the proposed community alignment algorithm achieves 3-8% better results in terms of semantic similarity as compared to previous local aligners. The average connectivity and coverage of the proposed algorithm are also better than the existing aligners.</p>","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":" ","pages":"4174-4182"},"PeriodicalIF":2.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139424819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}