Muhammad Shafiq , Bin Amin , Muhammad Awais Jehangir , Aijaz Rasool Chaudhry , G. Murataza
{"title":"First-principle calculations to investigate mechanical and acoustical properties of predicted stable halide Perovskite ABX3","authors":"Muhammad Shafiq , Bin Amin , Muhammad Awais Jehangir , Aijaz Rasool Chaudhry , G. Murataza","doi":"10.1016/j.jmgm.2024.108861","DOIUrl":"10.1016/j.jmgm.2024.108861","url":null,"abstract":"<div><p>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 TlBeF<sub>3</sub>, BaAgBr<sub>3</sub>, and CsTcl<sub>3</sub>—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 SrLiF<sub>3</sub>. The estimated Poisson's ratio data indicates the metallic bonding nature of HPs, whereas only SrLiF<sub>3</sub> exhibits covalent behavior with ν = 0.23. Debye temperature for SrLiF<sub>3</sub>, ZnLiF<sub>3</sub>, ZnScF<sub>3</sub>, CsRhCl<sub>3</sub>, CsRuCl<sub>3</sub>, and CsBeCl<sub>3</sub> 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 CaCuBr<sub>3</sub> (3.265) and lowest for SrLiF<sub>3</sub> (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.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108861"},"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}
Chuanhao Dong , Minglin Li , Yanyi Huang , Hai Yang , Bo Wu , Ruoyu Hong
{"title":"Molecular dynamics simulation study of graphene synthesis by rotating arc plasma","authors":"Chuanhao Dong , Minglin Li , Yanyi Huang , Hai Yang , Bo Wu , Ruoyu Hong","doi":"10.1016/j.jmgm.2024.108849","DOIUrl":"10.1016/j.jmgm.2024.108849","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108849"},"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}
Zunera Khalid , Amen Shamim , Mohamed J. Saadh , Ahmed Alafnan , Mohd Alaraj , Muhammad Hassan Butt , Tehreem Ashraf
{"title":"Identification of potential inhibitors against Corynebacterium diphtheriae MtrA response regulator protein; an in-silico drug discovery approach","authors":"Zunera Khalid , Amen Shamim , Mohamed J. Saadh , Ahmed Alafnan , Mohd Alaraj , Muhammad Hassan Butt , Tehreem Ashraf","doi":"10.1016/j.jmgm.2024.108858","DOIUrl":"10.1016/j.jmgm.2024.108858","url":null,"abstract":"<div><p><em>Corynebacterium diphtheriae</em> 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, <em>Corynebacterium diphtheriae</em> 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 <em>C. diphtheriae</em> 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 <em>C. diphtheria</em><em>e</em> infections. However, <em>in vivo</em> and <em>in vitro</em> animal experiments and accurate clinical trials are needed to validate the potential inhibitory effect of these compounds.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108858"},"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}
Lei Ma, Yukun Yan, Shaoxing Dai, Dangguo Shao, Sanli Yi, Jiawei Wang, Jingtao Li, Jiangkai Yan
{"title":"Research on prediction of human oral bioavailability of drugs based on improved deep forest","authors":"Lei Ma, Yukun Yan, Shaoxing Dai, Dangguo Shao, Sanli Yi, Jiawei Wang, Jingtao Li, Jiangkai Yan","doi":"10.1016/j.jmgm.2024.108851","DOIUrl":"10.1016/j.jmgm.2024.108851","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108851"},"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}
Tshele Mokhantso, Dean Sherry, Roland Worth, Ramesh Pandian, Ikechukwu Achilonu, Yasien Sayed
{"title":"Contrasting the effect of hinge region insertions and non-active site mutations on HIV protease-inhibitor interactions: Insights from altered flap dynamics","authors":"Tshele Mokhantso, Dean Sherry, Roland Worth, Ramesh Pandian, Ikechukwu Achilonu, Yasien Sayed","doi":"10.1016/j.jmgm.2024.108850","DOIUrl":"10.1016/j.jmgm.2024.108850","url":null,"abstract":"<div><p>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.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"133 ","pages":"Article 108850"},"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}
Lennin Isaac Garrido-Palazuelos , Arath Andrés Almanza-Orduño , Maaz Waseem , Amina Basheer , José Andrés Medrano-Félix , Mamuna Mukthar , Haris Ahmed-Khan , Fatima Shahid , José Roberto Aguirre-Sánchez
{"title":"Immunoinformatic approach for multi-epitope vaccine design against Staphylococcus aureus based on hemolysin proteins","authors":"Lennin Isaac Garrido-Palazuelos , Arath Andrés Almanza-Orduño , Maaz Waseem , Amina Basheer , José Andrés Medrano-Félix , Mamuna Mukthar , Haris Ahmed-Khan , Fatima Shahid , José Roberto Aguirre-Sánchez","doi":"10.1016/j.jmgm.2024.108848","DOIUrl":"10.1016/j.jmgm.2024.108848","url":null,"abstract":"<div><p><em>Staphylococcus aureus</em> 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 <em>S. aureus</em> infections typically involves the use of antibiotics. However, the emergence of antibiotic-resistant strains has become a major concern. Therefore, vaccination against <em>S. aureus</em> 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 <em>S. aureus</em> has proven to be challenging. This study aimed to use <em>in silico</em> methods to design a multi-epitope vaccine against <em>S. aureus</em> 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 <em>S. aureus</em>. Overall, these findings provide valuable insights into the design of an effective multi-epitope vaccine against <em>S. aureus</em> infection and pave the way for future experimental validations.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108848"},"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}
Junkai Wang , Jingyi Xing , Yifei Wang , Xin Zhang , Shaowei Zhang
{"title":"First-principles study of electrochemical H2O2 production on Pd-B40 single-atom catalyst","authors":"Junkai Wang , Jingyi Xing , Yifei Wang , Xin Zhang , Shaowei Zhang","doi":"10.1016/j.jmgm.2024.108847","DOIUrl":"10.1016/j.jmgm.2024.108847","url":null,"abstract":"<div><p>Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), a versatile green compound, is increasingly in demand. The electrochemical two-electron oxygen reduction reaction (2e<sup>−</sup> ORR) is a simple and environmentally friendly substitute method to the traditional anthraquinone oxidation method for H<sub>2</sub>O<sub>2</sub> production. This study systematically investigates the 2e<sup>−</sup> ORR process on single transition metal atom-loaded boron fullerene (M − B<sub>40</sub>) 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 B<sub>40</sub> exhibit good stability. Among these, Pd-modified B<sub>40</sub> heptagonal cavity (Pd-B<sub>40</sub>-heptagonal) demonstrates an ideal Gibbs free energy change for OOH* (4.49 eV) and efficiently catalyzes H<sub>2</sub>O<sub>2</sub> production at a low overpotential (0.27 V). Electronic structure analysis reveals that electron transfer between Pd-B<sub>40</sub>-heptagonal and adsorbed O<sub>2</sub> facilitates O<sub>2</sub> activation. Additionally, the high 2e<sup>−</sup> ORR activity of Pd-B<sub>40</sub>-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<sup>−</sup> ORR.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108847"},"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}
Albert Neil G. Dulay , John Christian C. de Guzman , Zyra Ysha D. Marquez , Elisha Sofia D. Santana , Jessamine Arce , Fredmoore L. Orosco
{"title":"The potential of Chlorella spp. as antiviral source against African swine fever virus through a virtual screening pipeline","authors":"Albert Neil G. Dulay , John Christian C. de Guzman , Zyra Ysha D. Marquez , Elisha Sofia D. Santana , Jessamine Arce , Fredmoore L. Orosco","doi":"10.1016/j.jmgm.2024.108846","DOIUrl":"10.1016/j.jmgm.2024.108846","url":null,"abstract":"<div><p>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 <em>in silico</em> screening of secondary metabolites (127) from <em>Chlorella</em> spp. The metabolites were screened for affinity and binding selectivity. High-scoring compounds were assessed through <em>in silico</em> 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 <em>in vitro</em> screening to develop potent antiviral drugs against ASFV.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108846"},"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}
{"title":"Hex-star phosphorene nanosheets as sequencing material for DNA/RNA strands – A first-principles investigation","authors":"V. Nagarajan , N. Reseeka , R. Chandiramouli","doi":"10.1016/j.jmgm.2024.108845","DOIUrl":"10.1016/j.jmgm.2024.108845","url":null,"abstract":"<div><p>In this study, we utilised hex-star phosphorene as the main detecting material to identify the nucleobases. Nucleobases, being crucial carriers of hereditary information are identified through specific hydrogen bonding and steric interactions such as adenine pairing with thymine (or) uracil and guanine pairing with cytosine. The stable hex-star phosphorene possesses negative formation energy of −5.194 eV. The hex-star phosphorene exhibits a semiconductor nature with an energy band gap of 1.658 eV, which is deployed as the adsorbing substrate for nucleobases. Based on the Mulliken charge analysis, adsorption energy, relative band gap variation, and the detection efficiency of hex-star phosphorene towards nucleobases are examined. The outcome confirms the physisorption of nucleobases on hex-star phosphorene and strongly supports that hex-star phosphorene can be used as sequencing material for <span>DNA</span> and RNA.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108845"},"PeriodicalIF":2.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141978769","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":"Combining machine learning, molecular dynamics, and free energy analysis for (5HT)-2A receptor modulator classification","authors":"Xian Yu, Yasmine Eid, Maryam Jama, Diane Pham, Marawan Ahmed, Melika Shabani attar, Zainab Samiuddin, Khaled Barakat","doi":"10.1016/j.jmgm.2024.108842","DOIUrl":"10.1016/j.jmgm.2024.108842","url":null,"abstract":"<div><p>The 5-Hydroxytryptamine (5HT)-2A receptor, a key target in psychoactive drug development, presents significant challenges in the design of selective compounds. Here, we describe the construction, evaluation and validation of two machine learning (ML) models for the classification of bioactivity mechanisms against the (5HT)-2A receptor. Employing neural networks and XGBoost models, we achieved an overall accuracy of around 87 %, which was further enhanced through molecular modelling (MM) (<em>e.g.</em> molecular dynamics simulations) and binding free energy analysis. This ML-MM integration provided insights into the mechanisms of direct modulators and prodrugs. A significant outcome of the current study is the development of a ‘binding free energy fingerprint’ specific to (5HT)-2A modulators, offering a novel metric for evaluating drug efficacy against this target. Our study demonstrates the prospective of employing a successful workflow combining AI with structural biology, offering a powerful tool for advancing psychoactive drug discovery.</p></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"132 ","pages":"Article 108842"},"PeriodicalIF":2.7,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991379","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}