Identification of <i>Streptococcus pneumoniae</i> Sortase A Inhibitors and the Interactive Mechanism by Guizhen Wang, Jiahui Lu, Jingyao Wen, Yifan Duan, Hanbing Zhou, Xinli Peng, Zhandong Li

“…The results showed that these inhibitors bound to the active pocket of SrtA, and the root mean square deviation (RMSD) and distance analyses showed that these compounds and SrtA maintained stable configuration and binding during the assay. …”
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Deterministic Calculation Method for Continuous-energy Neutron Transport Equation in No-resonance Energy-range by LIU Haopo, LI Yunzhao, WU Hongchun, CAO Liangzhi

“…On the one hand, thermal neutrons were affected by the target nuclear thermal motion, chemical bond binding and scattering wave interference effect, leading to the phenomenon of up-scattering. …”

Photo-catalytic degradation of Rhodamine 6G under visible lamp using citrate stabilized ZnO nanoparticles by M.A. Moreki, G.G. Matlou, N. Rapulenyane

“…The IR spectrum showed a stretching band at ≈650 cm−1 due to the ZnO bond and another vibrating band of ZnO at 875 cm−1, and a broad peak at 2925 cm−1 for the OH (Acid) group, and 1600 cm−1 for unsaturated (C=C). …”
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Epidemiology of Spinal Cord Injury in British Columbia, Canada: 20 Years of Population-Based Administrative Data by Michael Bond, Aidan Beresford, Vanessa Noonan, Naama Rotem-Kohavi, Marcel Dvorak, Brian Kwon, Guiping Liu, Jason M. Sutherland

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Identification and exploration of novel FGFR-1 inhibitors in the Lotus database for Cholangiocarcinoma (CCA) treatment by Samuel Aduramurewa Osunnaya, Wilberforce K. Ndarawit, Ifeoluwa Aderibigbe, Ibilola A. Omolopo, Precious O. Aribisala, Ayodele Oluwasegun Elekan, Adeola Sakirat Adeyemo, Sheriffdeen Abiola Amoo, Olatunde Simbiat Olamiposi, Njogu M. Kimani, Taiwo Hamidat Olaide, Adedoyin John-Joy Owolade, Damilola Samuel Bodun

“…Additionally, 100-ns molecular dynamic simulations demonstrated that the top three compounds remained stable within FGFR1's active site, supported by root mean square deviation, root mean square fluctuation, and hydrogen bond interactions. …”
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In Silico Analysis of Coding/Noncoding SNPs of Human RETN Gene and Characterization of Their Impact on Resistin Stability and Structure by Lamiae Elkhattabi, Imane Morjane, Hicham Charoute, Soumaya Amghar, Hind Bouafi, Zouhair Elkarhat, Rachid Saile, Hassan Rouba, Abdelhamid Barakat

“…The 3D structure of human resistin was generated by homology modeling using Swiss model. Root-mean-square deviation (RMSD), hydrogen bonds (h-bonds), and interactions were estimated. …”
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Regulation of magnetocaloric properties and critical behavior of La0.7Sr0.3MnO3 by high-pressure heat treatment by Xiang Jin, Huaijin Ma, Qi Li, Jiawei Xu, Jianjun Zhao, Tegus O, Jiaohong Huang

“…The nonlinear changes in average bond length with pressure were defined in two stages: 0–2 GPa (S1) and 2-4-6 GPa(S2). …”
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In-silico design and evaluation of quinoline-dione derivatives as Mycobacterium tuberculosis DprE1 inhibitors by Maimuna Shehu Rufa’i, Ibrahim A. Abdulganiyyu, Abduljelil Ajala, Mohnad Abdalla, Reham M. Alahmadi, Maaweya E. Awadalla, Khadija Abdulganiyyu, Asma’u Mahe, Yahaya Sa’id Gwarzo, Nafisatu Kabir

“…Stable binding was indicated by critical metrics such as root mean square deviation (RMSD) and root mean square fluctuation (RMSF). …”
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Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach by Saurav Kumar Mishra, Neeraj Kumar, Zsolt Tóth, Yousef A. Bin Jardan, Shopnil Akash, John J. Georrge

“…The stability was examined over 200 simulations via Desmond software, and trajectories were analyzed, followed by Root mean square deviation (RMSD), root mean square fluctuation (RMSF), and the radius of gyration (Rg), PCA (principal component analysis), etc., to assess their stability and interaction dynamics. …”
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Repurposed drugs as histone deacetylase 8 inhibitors: Implications in cancer and neuropathological conditions by Mohammed Alrouji, Kumar Venkatesan, Mohammed S. Alshammari, Fahad A. Alhumaydhi, Sheeba Shafi, Sharaf E. Sharaf, Moyad Shahwan, Anas Shamsi

“…The elucidated molecules were further evaluated for 500 ns long-run molecular dynamics (MD) simulation with HDAC8. Structural deviation, compactness, folding behavior, hydrogen bonds analysis, and secondary structure content profiling revealed complex stability formed by HDAC8 and the selected compounds. …”
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Structure based in silico screening of natural Vitamin D analogs for targeted and safer treatment of resistant multiple sclerosis by Mohtashim Lohani, Nizar Ahmad Khamjan, Sajad Ahmad Dar, Farrukh Aqil, Saif Khan, Arshad Jawed, Saba Beigh, Taru Singh, Iffat Zareen Ahmad

“…Both analogs formed consistent hydrogen bonds, exhibited low Root Mean Square Deviation (RMSD) values, minimal Root Mean Square Fluctuation (RMSF), and stable Solvent Accessible Surface Area (SASA), indicating robust ligand-receptor binding. …”
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Phytobioinformatics screening of ayurvedic plants for potential α-glucosidase inhibitors in diabetes management by Hira Khalid, Muhammad Hassan Butt, Aziz ur Rehman Aziz, Iqra Ahmad, Farzana Iqbal, Amen Shamim, Umar Nishan, Riaz Ullah, Mohamed A. Ibrahim, Arlindo Alencar Moura, Mohibullah Shah, Wenwen Sun

“…The stability of the interactions between the ligands and receptor protein was evaluated through Molecular Dynamic (MD) simulation trajectories including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), H bonds, β-factor analysis, and binding energy calculation through MM/GBSA method. …”
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Enhancement in Performance and Reliability of Fully Transparent a-IGZO Top-Gate Thin-Film Transistors by a Two-Step Annealing Treatment by Shuaiying Zheng, Chengyuan Wang, Shaocong Lv, Liwei Dong, Zhijun Li, Qian Xin, Aimin Song, Jiawei Zhang, Yuxiang Li

“…The <i>V</i>_th deviation (Δ<i>V</i>_th) was −0.032 V and −0.044 V, respectively, after a 7200 s positive and negative bias stress under the gate bias voltage <i>V</i>_G = ±3 V and <i>V</i>_D = 0.1 V. …”
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Identification of Potential Inhibitors Targeting Non-Structural Proteins NS3 and NS5 of Dengue Virus Using Docking and Deep Learning Approaches by Alomgir Hossain, Faria Tasnin Joti, Md. Shohag Hossain, Abdullah Al-Noman, Chomong Thowing, Mehjabin Mursona, Md. Robiul Islam, Md. Ekhtiar Rahman, Mohammad Nurul Matin, Md Azizul Haque

“…Further, molecular dynamics (MD) simulations were conducted to evaluate the root mean square deviation, root mean square fluctuation, solvent-accessible surface area, radius of gyration, and hydrogen bond count of the compounds. …”
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Effect and Mechanism of Aloin in Ameliorating Chronic Prostatitis/Chronic Pelvic Pain Syndrome: Network Pharmacology and Experimental Verification by Li R, Wang Y, Lao Y, You C, Qing L, Guan X, Wang J, Li X, Li Q, Liu S, Dong Z

“…Molecular dynamics simulations further validated binding stability by analyzing Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), hydrogen bonds, Solvent Accessible Surface Area (SASA), and Gibbs free energy of Aloin-target complexes. …”
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Phytochemical profiling and in silico evaluation of Artemisia absinthium compounds targeting Leishmania N-myristoyltransferase: molecular docking, drug-likeness, and toxicity analy... by Farouk Boudou, Amal Belakredar, Alaeddine Berkane, Ahcen Keziz, Huda Alsaeedi, David Cornu, Mikhael Bechelany, Mikhael Bechelany, Ahmed Barhoum

“…MD simulations confirmed the stability of the NMT-apigenin complex, with root mean square deviation (RMSD) values of 0.04 nm, root mean square fluctuation (RMSF) values between 0.05 and 0.35 nm, and radius of gyration (Rg) values ranging from 2.24 to 2.30 nm. …”
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Green Synthesis of Camellia sinensis-mediated Selenium-doped Vitamin E and Chitosan Nanoparticles along with Evaluation of their Anti-inflammatory and Anticancer Activity: An Ex-vi... by Shubhasri Arunachalam Sankaranarayanan, Anitha Roy, Muthuvel Surya

“…Fourier Transform Infrared (FTIR) spectroscopy identified molecular bonds corresponding to C-I stretching, C-H, C-O and C=O groups in the SeNPs-VitE/Chi. …”
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Cellular S Values and DNA Damage Induced by 125I Auger Electron and Tritium β-rays by SHEN Jiangyan1, ZHU Kun1, LI Qing1, ZHANG Desong1, LI Junli2, 3, YAN Congchong1

“…The S(N←N) derived from the uniform distribution of 125I and tritium in the cell nucleus, closely align with the published data, while those from radionuclide distribution in the cytoplasm S(N←Cy) deviate significantly, with the deviation from 4.23% to 26.35%. …”

Encapsulation of menthol by cyclodextrins-comparison between experiments and molecular simulations by Sa Xu, Fang Wei, Ximing Xu, Rui Wang, Xiujuan Xu, Wu Fan, Guobi Chai, Qidong Zhang, Qingzhao Shi

“…Conformation changes, root mean square deviation (RMSD), radius of gyration (Rg), Radial distribution function (RDF), solvent accessible surface area (SASA), and hydrogen bonds, and binding free energy were analyzed through molecular dynamics simulation and compared with the experimental results. …”
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Study on the mechanism of KRAS R68G secondary mutation-induced resistance to KRASG12D-targeted inhibitor MRTX1133 by WANG Gaoming, CUI Ran, LI Yanjing, LIU Yingbin

“…The number of hydrogen bonds between regions and the dynamic cross-correlation matrix (DCCM) of amino acid movements were also calculated.Results·RMSD analysis showed greater structural variation in KRAS in the KRASG12D/R68G system compared to the KRASG12D system. …”
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