Journal of Molecular Modeling最新文献

{"title":"Effect of gold slab layers relaxation on adsorption of alkanethiols on the (111) surface: a density functional theory study.","authors":"Walid Iken, Hayat El Ouafy, Loubna Halil, Soukaina Naciri, Mouad Boutkbout Nait Moudou, Mouna Aamor, Mohamed Reda Chriyaa, Tarik El Ouafy","doi":"10.1007/s00894-025-06404-w","DOIUrl":"https://doi.org/10.1007/s00894-025-06404-w","url":null,"abstract":"<p><strong>Context: </strong>Despite numerous studies on alkanethiol adsorption on gold surfaces, this work uniquely investigates the impact of Au(111) surface layers relaxation on adsorption energy, electrical conductivity, and molecular geometry using density functional theory (DFT). We demonstrate that adsorption energy increases linearly with increasing relaxation layers. Notably, relaxing only the top layer yields a slope close to experimental data. Geometrically, molecules exhibit greater tilt on a fully frozen surface, except methanethiol. In terms of electrical conductivity, gap energy decreases upon adsorption when all layers are frozen. Furthermore, Fermi energy rises exponentially with adsorption energy for a frozen surface but follows a linear trend with relaxation. These insights offer a deeper understanding of surface effects on molecular adsorption.</p><p><strong>Methods: </strong>Adsorption energies and geometric parameters were calculated by DFT with QUANTUM ESPRESSO, using GGA-PBE and Grimme D3 for van der Waals corrections. Core-valence interactions were described by PAW and pseudopotentials. Au(111) slab, constructed with VESTA, contained 3 layers.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"182"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214580","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 research on tricyclic-based as high-energy performance energetic materials.","authors":"Shaoqing Wang, Yan Huang, Qing Ma, Fu-Xue Chen","doi":"10.1007/s00894-025-06401-z","DOIUrl":"https://doi.org/10.1007/s00894-025-06401-z","url":null,"abstract":"<p><strong>Context: </strong>A series of tricyclic high energy density materials (HEDMs) incorporating diazole, triazole, and tetrazole frameworks were systematically investigated through density functional theory (DFT) calculations at the B3LYP/6-31G +  + (d,p) and M06-2X/def2-SVP levels. Nitroform-based compounds and fluorodinitromethyl-substituted derivatives were found to exhibit superior densities compared to HMX. Notably, compound II-7 demonstrated the highest predicted density of 2.04 g cm⁻³, along with optimal detonation performance (D = 9451 m s⁻¹, P = 42.57 GPa), surpassing that of HMX. Regarding heat of formation, the tetrazole-based compound III-1 exhibited the highest value of 844.42 kJ mol⁻¹, suggesting enhanced energy content. While nitroform groups improve performance, fluorine substitution offers better stability and sensitivity, representing an effective optimization strategy for energetic materials. Comparative analysis of structures with identical substituents but different parent ring frameworks reveals clear structure property relationships. The incorporation of nitrogen oxygen bonds is shown to significantly enhance performance characteristics.</p><p><strong>Method: </strong>Based on the DFT, molecular optimization and performance metrics analysis were all calculated using the Gaussian 09 package at B3LYP/6-31G +  + (d,p) and M06-2X/def2-SVP levels. The electrostatic potential energy and other related calculations were computed using Multiwfn_3.8_dev software. The visualization of the weak interaction between dimers was accomplished using VMD 1.9.3 program.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"183"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214584","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":"Fused pyrido[3,4-D]pyrimidine moiety with phthalazinone ring accelerate dual inhibition of PARP1 and CDK4 in triple-negative breast cancer: a hybrid design with computational investigation through molecular modeling and quantum mechanics.","authors":"Mahema Sivakumar, Jency Roshni, Sheikh F Ahmad, Sabry M Attia, Magesh Ramasamy, Shiek S S J Ahmed","doi":"10.1007/s00894-025-06393-w","DOIUrl":"https://doi.org/10.1007/s00894-025-06393-w","url":null,"abstract":"<p><strong>Context: </strong>The PARP inhibitor olaparib is effective in breast cancer patients; however, its efficacy is reduced in triple-negative breast cancer (TNBC) due to mechanisms of drug resistance. Recent studies demonstrate that the CDK4 inhibitor palbociclib can enhance the sensitivity of cancer cells to PARP inhibitors. We designed 43 hybrid compounds by combining the pyrido[3,4-d]pyrimidine moiety from palbociclib with the phthalazinone ring from olaparib. Pharmacokinetic profiling and molecular docking revealed compound 17 as a promising candidate, demonstrating a binding affinity of - 8.42 kcal/mol with PARP1 and - 10.05 kcal/mol with CDK4, in contrast to the native inhibitors. Furthermore, the induced fit docking validated its superiority compared to the native inhibitors. Molecular dynamics simulations over 500 ns confirmed the structural stability of compound 17 with both targets. Moreover, the QM/MM, DFT, TD-DFT, and MEP analyses yielded significant insights into charge transfer and electronic transitions, augmenting our understanding of the electronic and bonding properties of the hybrid compound.</p><p><strong>Methods: </strong>To facilitate the design of 43 hybrid compounds, ChemSketch was utilized, and QikProp, a module of the Maestro Schrödinger suite (v13.5), was used to make predictions regarding the pharmacokinetic properties of these compounds. We checked the binding affinities using docking methods and the stability of the protein-ligand complex using molecular dynamics simulations with Desmond module in Maestro Schrödinger suite (v13.5). Quantum mechanical analyses at the B3LYP/6-31G** level were conducted to elucidate the DFT/TD-DFT, molecular electrostatic potential, Mulliken charges, chemical descriptors, NBO, and NLO properties.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"181"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214582","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":"The K⁺/Y³⁺ cationic exchange in a C₅-symmetric metallamacrocyclic scaffold: DFT examination with QTAIM, ELF, MEP approaches and XRD study of the final alaninehydroximate complex.","authors":"Grigory Zhigulin, Galina Zabrodina, Evgeny Baranov, Marina Katkova, Sergey Ketkov","doi":"10.1007/s00894-025-06409-5","DOIUrl":"https://doi.org/10.1007/s00894-025-06409-5","url":null,"abstract":"<p><strong>Context: </strong>Participation of the heterobimetallic potassium-copper metallamacrocycle in synthesis of the yttrium-copper C₅-symmetric complex based on the L-α-alaninehydroximate (Alaha) ligands was investigated by DFT. Two possible conformations of the K(I)-Cu(II) intermediate which can realize in solution were simulated. Theoretical estimations of an activation barrier for the conformational conversion, ∆G^≠_sol(298.15) = 2.7 and 1.0 kcal/mol, indicate a structural inversion of the encapsulated K⁺ ion relative to the copper-containing metallamacrocyclic environment (scaffold). The K(I)-Cu(II) intermediate is considered as a handy molecular platform for facile chelation of the Y³⁺ ions in water solutions that can be used in the nuclear medicine. Replacement of the K⁺ central ion by Y³⁺ is driven by the higher positive charge of the latter which makes it a stronger acceptor of the metallamacrocyclic electron density. Corresponding changes in the electron structure were revealed and quantified by the DFT calculations. Also, the theoretical thermodynamic estimations predict enhanced stability of the final Y(III)-Cu(II) metallamacrocycle. Accordingly, the water-soluble Y(III)-Cu(II) alaninehydroximate complex was prepared in the presence of K₂CO₃ as one of starting reagents.</p><p><strong>Methods: </strong>The quantum chemical calculations were performed at the M06/def2-TZVP and TPSS-D3/def2-TZVP levels of DFT with use of the polarizable continuum model. The differences in the electron structures were investigated in detail by the quantum theory of atoms in molecules, electron localization function, and molecular electrostatic potential. The final product of the Y(CO₃)(H₂O)[15-MC_Cu(II)Alaha-5](I)∙11H₂O composition was characterized by the X-ray diffraction.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 7","pages":"180"},"PeriodicalIF":2.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214583","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":"Geometrical and electronic structures, stability, and aromaticity of copper-doped boron clusters B_nCu^0/- (n = 1-13).","authors":"Nguyen Huu Tho, Ngo Huyen Tran, Pham Hong Cam, Nguyen Minh Tam","doi":"10.1007/s00894-025-06381-0","DOIUrl":"10.1007/s00894-025-06381-0","url":null,"abstract":"<p><strong>Context: </strong>Besides small pure boron clusters which have been well studied, doped boron clusters, in particular with transition metal dopants, are also increasingly investigated due to their unique geometrical structures accompanied by novel physical and chemical properties. However, studies on copper-doped boron clusters are still scarce despite copper being a transition metal with important properties. In this context, the geometry, stability, and electronic properties of copper-doped boron clusters B_nCu^0/- (n = 1-13) were systematically studied. The obtained results show that the geometries of neutral and anionic clusters are very similar only at sizes n = 2, 5, 6, 8, and 10. In the ground state, both neutral and anionic clusters tend to be in the low-spin state, except for B₂Cu^- and B₆Cu^-. The relative stability of these structures was evaluated using various energetic parameters. Moreover, the aromaticity of the B₈Cu^- anion along with its enhanced stability are also discussed and rationalized in detail.</p><p><strong>Method: </strong>In this work, the geometry optimization and the following molecular orbital analyses of B_nCu^0/- (n = 1-13) structures are performed using density functional theory (DFT), specifically the hybrid functional TPSSh combined with the 6-311+ G(d) basis set for boron atoms and the aug-cc-pVTZ-PP basis set for a copper atom. To obtain more reliable results, the single point energies of some lowest lying isomers whose relative energy values are close corresponding to geometries optimized at the TPSSh/6-311+ G(d) (B) / aug-cc-pVTZ-PP (Cu) level were determined with higher precision at the CCSD(T) level with the same basis sets. Based on the obtained results at the DFT level, the energetic parameters are determined to elucidate thermodynamic stability of B_nCu clusters. NICS and ELF indices, the density of states, and AdNDP bond analysis are then examined to rationalize the aromaticity of the anion B₈Cu^-. All calculations were performed using the Gaussian 09 and Multiwfn programs.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":"179"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186192","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":"Water catalyzed atmospheric oxidation of 1,1,2,2- tetrafluoroethene (TFE) with ozone: a computational study.","authors":"Kamal Kant Rav, Kumari Sonika, Ekta Sonker, Pradeep Kumar Rao","doi":"10.1007/s00894-025-06400-0","DOIUrl":"10.1007/s00894-025-06400-0","url":null,"abstract":"<p><strong>Context: </strong>1,1,2,2- tetrafluoroethene (TFE) is a class of per fluoroalkenes. The reaction of TFE with ozone is significant in the atmospheric oxidation of per fluoroalkenes. Kinetics of TFE + O₃ reaction in absence of as well as in presence of single water molecule act as catalyst has been analysed in gas phase as well as in solvent phase. The impact of water solvated environment is demonstrated to be significant to the extent that even single water molecules can function as catalysts in the ozonolysis of titled molecule. The computations related to the coordination of a single water molecule illustrate distinctly the notable decrease in the energy barrier and the substantial lowering of the activation energy. The investigation revealed that the mechanism of this reaction, which is facilitated by water as catalyst presents greater kinetic benefits compared to its non-catalytic counterpart. Calculated rate constant for water catalyzed and non catalyzed ozonolysis of titled molecule were estimated to be 1.0 × 10^-16 cm³molecule^-1 s^-1 and 3.0 × 10^-17 cm³molecule^-1 s^-1respectively. The atmospheric lifetimes, radiative forcing and global warming potential (GWP) have been determined as well.</p><p><strong>Methods: </strong>All electronic structure calculations have been done employing Gaussian 09 software package. Geometry optimizations and frequency calculations have been performed using DFT/M06-2X/6-311 + G(d,p) method. The energies were further refined and potential energy were constructed at CCSD(T)/6-311 + G(d,p) level.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":"177"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186195","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 dynamics simulations for the sensitivity and moisture adsorption on the surface of a novel cocrystal: CL-20/DNAN.","authors":"Yuqing Zhang, Jingtao Wang","doi":"10.1007/s00894-025-06396-7","DOIUrl":"10.1007/s00894-025-06396-7","url":null,"abstract":"<p><strong>Context: </strong>Cocrystals are recognized as an effective strategy to mitigate the high sensitivity of energetic materials. In this paper, we use molecular dynamics (MD) to simulate the binding energies and XRD of CL-20/DNAN cocrystals with different ratios to prove that there is a new type of cocrystal structure between CL-20 and DNAN. To further investigate the effect of moisture absorption on the storage safety of cocrystals, this paper simulates the adsorption process of water molecules on the (0 0 1), (0 1 0), (1 0 0) crystal surfaces, respectively. By analyzing the radial distribution function plots, it is found that there are hydrogen bonding interactions between water molecules and molecules on the surface of the cocrystal, and the (1 0 0) face is most likely to adsorb water molecules. By analyzing the length of the triggering bond and the cohesive energy density of the cocrystal, it was found that when water molecules are absorbed on the surface, the N-NO2 bond of the cocrystal explosive is more likely to be broken and the sensitivity of the explosive is higher on the surface, leading to increased sensitivity.</p><p><strong>Methods: </strong>The MD simulation is conducted utilizing the Materials Studio software, operating under the NPT set with a temperature of 298 K, a pressure of 0.0001 GPa, temperature control of Andersen, and pressure control of Berendsen. The simulation spans a duration of 150 ps, with samples being recorded at an interval of 1 fs throughout the computational process. Similar simulations are conducted for all systems.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":"178"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186193","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":"Simulation study of hardness via nanoindentation of polymer nanocomposites through molecular dynamics.","authors":"Eduardo Naranjo-Adorno, Edgar O Castrejón-González, Juan F J Alvarado, Christian O Díaz-Ovalle, Vicente Rico-Ramírez","doi":"10.1007/s00894-025-06403-x","DOIUrl":"10.1007/s00894-025-06403-x","url":null,"abstract":"<p><strong>Context: </strong>Polyethylene (PE) and polylactic acid (PLA) are two of the most widely used polymers. It is known that their mechanical properties, such as hardness, are poor. In order to enhance the mechanical properties of those polymers, reinforcements have to be incorporated. Carbon nanotubes (CNTs) have proven to be an excellent choice for reinforcement. However, due to the π-π interactions, the nanotubes tend to agglomerate. One of the strategies to avoid agglomerations is chemical functionalization. The 3-amino-propyl tri-ethoxy silane (APTES) is a suitable option for functionalization. In this work, three different polymeric configurations were analyzed to verify their effect on hardness: linear, hyperbranched, and star-like. Further, the configuration with the highest hardness was reinforced with functionalized CNTs with APTES groups. Results indicate that a linear configuration, both of PE and PLA, generates greater hardness due to better structural arrangement. The percentage of functionalization of CNTs that generates a better interaction with PLA is 3%, which corresponds to five anchored groups. The addition of CNTs increases the hardness 14 times with respect to that of PLA without reinforcement.</p><p><strong>Method: </strong>Molecular models were built and visualized using MedeA and OVITO software programs. All simulations were run using the LAMMPS software. The force fields utilized were PCFF for polyethylene and COMPASS for PLA and carbon nanotubes. A van der Waals model was used to consider the non-bonding interactions between the indenter and substrate. An NVT ensemble was used to construct the substrates, and the indentation procedure involved iterative cycles of minimization and displacement of the indenter.</p>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":"176"},"PeriodicalIF":2.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186194","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":"Electronic excitation behavior and anharmonic IR spectrum characteristics of RDX","authors":"Xinrui Zhang,&nbsp;Zhiyue Han","doi":"10.1007/s00894-025-06398-5","DOIUrl":"10.1007/s00894-025-06398-5","url":null,"abstract":"<div><h3>Context</h3><p>RDX, a typical nitro-based energetic material, has a wide range of applications. In recent years, the frequent occurrence of production accidents has created an urgent need for effective early detection technologies, which rely heavily on its spectral characteristics. This research systematically discusses the ultraviolet spectrum and electronic excitation behavior of RDX using charge transfer spectrum, hole-electron analysis, and NBO analysis methods. It also conducts anharmonic calculations to systematically explore various vibrational forms related to the -NO₂ characteristic bands in the infrared spectrum of RDX. Additionally, considering the requirements of actual production scenarios, the impact of solvents on spectral changes is examined. The findings can provide a theoretical basis for the safe production detection methods of energetic materials.</p><h3>Method</h3><p>All calculations on the structures and NBO analysis were conducted using Gaussian 16 software. Additionally, further calculations on electronic excitations were performed using Multiwfn, while VMD was employed for visualization.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140161","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 comprehensive review on structural insights through molecular visualization: tools, applications, and limitations","authors":"Ved Vrat Verma,&nbsp;Swapnil Vimal,&nbsp;Manoj Kumar Mishra,&nbsp;Varun Kumar Sharma","doi":"10.1007/s00894-025-06402-y","DOIUrl":"10.1007/s00894-025-06402-y","url":null,"abstract":"<div><h3>Context</h3><p>Biomolecules serve as intrinsic repositories of information related to function, binding interactions, molecular motion, and structural conformations. With the rapid accumulation of structural data from fields such as structural biology and cheminformatics, the ability to visualize biomolecular architecture has become essential for researchers in biology, pharmacology, and related disciplines. Molecular visualization represents a foundational step in accessing and interpreting this data, enabling its application in diverse scientific and therapeutic contexts. Recent advancements in computational algorithms and web-based visualization platforms have provided powerful resources for structural biologists, chemists, and crystallographers, facilitating efficient analysis and reproducibility of experimental outcomes. This review offers a comprehensive overview of contemporary molecular visualization tools, emphasizing their practical applications. Particular attention is given to PyMOL and NGL Viewer, with detailed guidance for their implementation in visualizing proteins, DNA, protein–ligand complexes, protein–protein interactions, protein-DNA assemblies, and small molecule ligands. Challenges frequently encountered in structural biology and cheminformatics, such as the identification of lead compounds for therapeutic development, are also addressed. Molecular dynamics simulations, including binding free energy calculations, are discussed as cost- and time-effective strategies to enhance drug discovery pipelines. In response to the increasing complexity of data-driven research, this review aims to serve as a valuable resource for professionals seeking efficient, reliable visualization tools to support structure-based research and drug design.</p><h3>Methods</h3><p>This review article provides a comprehensive comparative analysis of biomolecular visualization features integrated into standalone and web-based molecular visualization tools. PyMOL (standalone) and NGL (web-based) were systematically employed to visualize proteins, ligands, protein–ligand complexes, protein–protein complexes, and protein-DNA complexes. The methodological framework outlined in this study establishes standardized guidelines for the effective utilization of molecular visualization tools, offering valuable insights for structural biologists and researchers engaged in molecular modeling and structural analysis.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 6","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140087","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}