Alpiniae oxyphyllae Fructus ameliorates renal lipid accumulation in diabetic kidney disease via activating PPARα by Zi-Jie Yan, Lin Zhang, Xin-Yao Han, Yu Kang, Shu-Man Liu, Tian-Peng Ma, Man Xiao, Yi-Qiang Xie

“…Results: Network pharmacological enrichment analysis, molecular docking, and molecular dynamics simulation showed that the active compounds in AOF targeted PPARα and thus transcriptionally regulated ACOX1 and CPT1A. …”
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An In Silico Study of the Interactions of Alkaloids from Cryptolepis sanguinolenta with Plasmodium falciparum Dihydrofolate Reductase and Dihydroorotate Dehydrogenase by Lois Kwane Kyei, Edward Ntim Gasu, Gilbert Boadu Ampomah, Jehoshaphat Oppong Mensah, Lawrence Sheringham Borquaye

“…Therefore, molecular docking and molecular dynamics simulations were used to investigate the interactions and stability of the alkaloids with PfDHFR and PfDHODH. …”
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Molecular origin of asymmetric yield surface of crosslinked epoxy polymers by Jinyoung Kim, Kyeongmin Hong, Yong-Seok Choi, Dayoung Jang, Jang-Woo Han, Hyungbum Park

“…In this study, we investigate the multiaxial mechanical behavior of thermosetting epoxy polymers and explore the asymmetry between tension and compression in their yield surfaces at the molecular level using molecular dynamics simulations, complemented by experimental validation through polymer synthesis. …”
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Interaction of α-Cembrenediol with Human Serum Albumin Based on Spectroscopic and Computational Analyses by Xian-Kun Su, Zhen-Chun Sun, Chang-You Zhao, Hui Yang, Tian-Ming Zhao, Chao Ma, Guo-Fei Zhu

“…To this end, we utilized various methods including UV absorption spectroscopy, steady-state fluorescence analysis, circular dichroism measurements, molecular docking studies, and molecular dynamics simulations. The results of the UV and fluorescence spectra clearly demonstrated that HSA interacts with α-cembrenediol. …”
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Virtual Screening, Toxicity Evaluation and Pharmacokinetics of Erythrina Alkaloids as Acetylcholinesterase Inhibitor Candidates from Natural Products by Permana A, Akili AWR, Hardianto A, Latip JB, Sulaeman AP, Herlina T

“…The top alkaloid, 8-oxoerymelanthine ( 128), was subjected to further analysis through molecular dynamics simulations, with the objective of evaluating its stability and interactions. …”
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Examining Prenylated Xanthones as Potential Inhibitors Against Ketohexokinase C Isoform for the Treatment of Fructose-Driven Metabolic Disorders: An Integrated Computational Approa... by Tilal Elsaman, Magdi Awadalla Mohamed

“…Molecular docking, binding free energy calculations, pharmacokinetic assessments, molecular dynamics simulations, and quantum mechani–cal analyses were used to screen and evaluate the compounds. α-Mangostin’s binding affinity (37.34 kcal/mol) served as the benchmark. …”
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Fracture-healing effects of Rhizoma Musae ethanolic extract: An integrated study using UHPLC-Q-Exactive-MS/MS, network pharmacology, and molecular docking. by Jian Zhang, Wanyan Shen, Fanzhi Liu, Hehe He, Shuquan Han, Lina Luo

“…Molecular docking and molecular dynamics simulations results demonstrated a strong binding affinity between the main compounds of EERM and key targets. …”
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Water Evaporation and Conformational Changes from Partially Solvated Ubiquitin by Saravana Prakash Thirumuruganandham, Herbert M. Urbassek

“…Using molecular dynamics simulation, we study the evaporation of water molecules off partially solvated ubiquitin. …”
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Evaluation of fluorinated phospholipid analogs: A study on ADMET profiles, molecular docking and dynamics simulation in anticancer therapy by Saqib Ishaq, Obaid Habib, Abdul Aziz, Raheel Tahir, Hira Mushtaq, Said Hassan, Sarah Sarwar, Mohammad S. Mubarak, Ajaz Ahmad, Amin Ullah

“…Using evolved computational approaches, this research evaluated their ADMET (absorption, distribution, metabolism, excretion and toxicity) profiles receptor binding affinities and molecular dynamics. Molecular docking discernible vigorous interactions with Edelfosine drug displaying greater binding stability and consistent hydrogen bonding as confirmed by 100 ns molecular dynamics simulations. …”
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Computational analysis of Allium sativum compounds to identify thermolabile hemolysin inhibitors against Vibrio alginolyticus in shrimp by Sayed Mashequl Bari, Nafees Bin Reza, Meamaching Marma, Sk. Foisal Ahmed, Md Arif Hussain, Md Naimuddin Jabed, Md Alomgir Hossain, Maria Manzoor, Md Saiful Alam

“…Various computational approaches, including molecular docking, pharmacokinetic analysis, and molecular dynamics simulation, were conducted to predict the compounds that can inhibit the phospholipase and hemolysis activities of the thermolabile hemolysin protein. …”
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Computational studies and structural insights for discovery of potential natural aromatase modulators for hormone-dependent breast cancer by Snehal Aditya Arvindekar, Sanket Rathod, Prafulla Balkrishna Choudhari, Pradnya Kiran Mane, Aditya Umesh Arvindekar, Suraj Narayan Mali, Bapu Thorat

“…QSAR studies were performed using the flavonoid compounds, in order to identify the structural functionalities needed to improve the anti-breast cancer activity. Molecular dynamics of the screened hits confirmed the stability of compounds with the target in the binding cavity. …”
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Nuclear Stopping in Central Au+Au Collisions at RHIC Energies by Ying Yuan, Nana Guan

“…Nuclear stopping in central Au+Au collisions at relativistic heavy-ion collider (RHIC) energies is studied in the framework of a cascade mode and the modified ultrarelativistic quantum molecular dynamics (UrQMD) transport model. In the modified mode, the mean field potentials of both formed and “preformed” hadrons (from string fragmentation) are considered. …”
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Computational insights into Sitahe (Leuconotis eugenifolia) bioactive compounds: A promising approach for radioprotection through p53 inhibition by Dian Pribadi Perkasa, Iin Kurnia, Taufik Muhammad Fakih, Teja Kisnanto, Dwi Ramadhani, Harry Nugroho Eko Surniyantoro, Boky Jeanne Tuasikal, Alfian Mahardika Forentin, Mukh Syaifudin

“…To evaluate the stability and reliability of these interactions, molecular dynamics (MD) simulations were performed over a duration of 500 ns. …”
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Dynamical Properties of the New Ternary Fission in Collisions of 197Au+197Au at 15 MeV/Nucleon by Xian Li, Chengqian Wang, Yaohui Xu

“…The dynamical properties of the new ternary fission in heavy 197Au+197Au at 15 MeV/nucleon have been investigated by using the improved quantum molecular dynamics model. The dependencies of the production probability, lifetime, the time interval, and angular distribution on the impact parameter are carefully studied. …”
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Generalized approach for rapid entropy calculation of liquids and solids by Qi-Jun Hong, Zi-Kui Liu

“…The proposed method utilizes a single trajectory of molecular dynamics (MD) to facilitate the calculation of entropy, which is composed of three components. …”
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Expression pattern of Calbindin-D28k, NeuN proteins, ATOH1 and EN2 genes in the human fetal cerebellum by Phanindra Prasad Poudel, Arnab Ghosh, Chacchu Bhattarai, Saman Pradhan, Nirmal Panthi, Dela Singh Joshi, Shanti Khadka, Sandhya Kumari, Guruprasad Kalthur, R. Vani Lakshmi, Sneha Guruprasad Kalthur

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Integrated analysis of bioinformatics, mendelian randomization, and experimental validation reveals novel diagnostic and therapeutic targets for osteoarthritis: progesterone as a p... by Ziyu Weng, Chenzhong Wang, Bo Liu, Yi Yang, Yueqi Zhang, Chi Zhang

“…The Drug Signatures Database (DSigDB) was utilized to screen small-molecule drugs targeting these hub genes, and molecular docking analyses and molecular dynamics simulations were employed to explore and validate the binding interactions between proteins and small-molecule drugs. …”
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Modeling phase equilibria for a water-CO2-hydrocarbon mixture using CPA equation of state in CO2 injection EOR-storage processes: a Colombian case study by Juan David Aristizábal Marulanda, Cristiam David Cundar Paredes, Christian David Guerrero Benavides, Andres Aguirre, Juan Andres Pasos, Ivan Dario Moncayo Riascos, Marco Ruiz, Pedro Nel Benjumea Hernández, William Mauricio Agudelo, Raúl Osorio Gallego

“…The associative parameters of the equation were taken from literature and estimated through molecular dynamics simulations of water-CO2-Hydrocarbon interactions. …”
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Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3 by Viktoria Korn, Kristyna Pluhackova

“…To unveil the process of their pore formation, we examine the energy landscapes upon insertion of the gasdermin D and A3 monomers into a lipid bilayer by extensive atomistic molecular dynamics simulations. We reveal a lower free energy barrier of membrane insertion for gasdermin D than for gasdermin A3 and a preference of gasdermin D for the membrane-inserted and of gasdermin A3 for the membrane-adsorbed state, suggesting that gasdermin D first inserts and then oligomerizes while gasdermin A3 oligomerizes and then inserts. …”
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Modeling the Mechanical Properties of Functionalized Carbon Nanotubes and Their Composites: Design at the Atomic Level by Qing-Sheng Yang, Bing-Qi Li, Xiao-Qiao He, Yiu-Wing Mai

“…Tension and compressive buckling behaviors of different configurations of CNTs functionalized by H atoms are studied by a molecular dynamics (MD) method. It is shown that H-atom functionalization reduces Young’s modulus of CNTs, but Young’s modulus is not sensitive to the functionalization configuration. …”
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