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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sat Jun 20 2020
Journal Name
Neuroquantology
Study of Charge Flow Coefficient Au Metal with a - NPD Molecule Dye
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The coefficient of charge transfer at heterogeneous devices of Au metal with a well-known dyeis investigations using quantum model.Four different solvent are used to estimation the effective transition energy. The potential barrier at interface of Au and dye has been determined using effective transition energy and difference between the Fermi energy of Au metal and ionization energy of dye. A possible transfer mechanism cross the potential barrier dyeand coupling strength interaction between the electronic levels in systems of Au and is discussed.Differentdata of effective transition energy and potential barrier calculations suggest that solvent is more suitable to binds Au with dye.

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Publication Date
Tue Jan 30 2024
Journal Name
Iraqi Journal Of Science
A Study of Drinking Water Properties in Some Hospitals in Baghdad City
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One of the bigger problems in drinking water is disinfection by-products (DBPs) that come from chlorinated disinfection. This study’s goal was to evaluate the drinking water in Al-Yarmouk Teaching Hospital, Ibn Sina Hospital and Ibn-Al-Nafis Hospital.  Samples were collected between October 2018 and September 2019. Physical and chemical characteristics of the water were studied, including (temperature, hydrogen ion (pH), total dissolved solids (TDS), electrical conductivity (EC), turbidity, free residual chlorine, total organic carbon (TOC), total trihalomethanes (THMs), total halo acetic acid (THAAs)). Data analysis showed the highest value of study temperature, pH, TDS, EC, turbidity, free residual chlorine and TOC which was

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Publication Date
Sun Mar 27 2022
Journal Name
Journal Of The College Of Basic Education
A Cross-Cultural Study of Criticism Strategies: Iraqi and Malay ESL Learners
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        Criticism, as an evaluative criterion, is a significant speech act for English language learners to improve their speech and actions in their academic life. Yet, it is realized differently across diverse cultures. Few studies have shown that the linguistics forms of one language are different from those available in another language. Hence, this study aims to investigate the cross-cultural similarities and differences between 60 Iraqi and Malay university learners in the use of criticism strategies. The data are collected using a Discourse Completion Test (DCT) and a Focus Group Interview (FGI). The data are coded based on Nguyen’s (2005) coding scheme of criticism in terms of the realization strategies. Qualitative

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Publication Date
Sun Feb 20 2022
Journal Name
Papers In Physics
Electronic and optical properties of nickel-doped ceria: A computational modelling study
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Cerium oxide CeO2, or ceria, has gained increasing interest owing to its excellent catalytic applications. Under the framework of density functional theory (DFT), this contribution demonstrates the effect that introducing the element nickel (Ni) into the ceria lattice has on its electronic, structural, and optical characteristics. Electronic density of states (DOSs) analysis shows that Ni integration leads to a shrinkage of Ce 4f states and improvement of Ni 3d states in the bottom of the conduction band. Furthermore, the calculated optical absorption spectra of an Ni-doped CeO2 system shifts towards longer visible light and infrared regions. Results indicate that Ni-doping a CeO2 system would result in a decrease of the band gap. Finally,

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Publication Date
Sun Feb 15 2026
Journal Name
Journal Of Physical Education
A Study of Actual Training Time Administration in Bedra Specialized Weightlifting Club
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Publication Date
Thu Mar 10 2022
Journal Name
Oral Surgery
Evaluation of buffered local anaesthesia in dental extraction: A randomized controlled study
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Buffering of Local anaesthesia (LA) has been suggested as a mechanism to improve injection comfort and hasten the onset of anaesthesia. Aim This study aimed to evaluate the effectiveness of buffered LA in the extraction of maxillary premolars and molars. Materials and Methods This randomized controlled study included 100 patients who were indicated for extraction of maxillary posterior teeth, they were randomly divided into two groups; a study group that received infiltration of buffered 2% lidocaine hydrochloride with 1:80,000 epinephrine LA, and a control group that received non-buffered 2% lidocaine hydrochloride with 1:80,000 epinephrine LA. The buffering was performed using the Onset® LA buffering system (Onpharma®). The outcome va

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Publication Date
Wed Mar 04 2015
Journal Name
Environmental Earth Sciences
Isotopic study of water resources in a semi-arid region, western Iraq
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Publication Date
Fri Nov 17 2023
Journal Name
Nasaq
A Semantic Study of Thematic Progression in Selected American and British Movies
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ZG Abdulrazaq, MR Younus, Nasaq, 2023

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Engineering
A Laboratory Study Attempt of Flow and Energy Dissipation in Stepped Spillways
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A new laboratory study conducted on stepped spillways in order to investigate their efficiency of dissipating flow energy. All previous study on stepped spillway indicated that the flow energy dissipation decreased as increasing in discharge. Increasing in the step numbers and the spillway slope led to energy dissipation decrease. In this study, an experimental attempt to increase energy dissipation at variable discharges was performed on stepped spillway and that leads to decreasing the cost of initiating the stilling basin or may be ignoring it. Five spillways were constructed from concrete and tested to investigate and compare among them. Three were roughed by gravel with different size for each one, one of them was s

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Publication Date
Sat Mar 09 2019
Journal Name
Journal Of Global Pharma Technology
Biological Activity Study of Schiff Base ligands and their Complexes: A Review
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Schiff bases (SBs) based on amino acid derivative stand for multipurpose ligands that formed by condensing amino acids with carbonyl groups. They are significant in pharmaceutical and medical areas due to their widespread biological actions such as antiseptic, antifungal, along with antitumor actions. Transition metallic complexes resulting from SB ligands with biological activity were extensively experimented in the literature. In this article, we review, in details, about synthesizing and biological performances of SBs along with its complexes.