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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 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.

Publication Date
Sun Jan 01 2023
Journal Name
Aip Conference Proceedings
Prevalence of polypharmacy among older adult patients in Baghdad: A descriptive study
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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
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
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
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
Tue Sep 09 2025
Journal Name
Journal Of Physical Education
A Study of Actual Training Time Administration in Bedra Specialized Weightlifting Club
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Publication Date
Mon Feb 28 2022
Journal Name
Journal Of Educational And Psychological Researches
Classroom Teachers’ Perceptions of Response to Intervention Implementation: a Qualitative Interview Study
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The purpose of this interview study was to explore teachers’ perceptions of Response to Intervention (RtI) implementation in their school. Particularly, the study explored teachers’ knowledge of RtI, teachers’ perceptions of RtI their intervention/instruction in school, and teachers’ suggestions of RtI implementation in their school. The study design was a qualitative interview in nature and data were collected from face-to-face interviews with four teachers in one school. The findings revealed that RtI means to identify students’ problems; the positive teachers’ perceptions of their implementation included: (a) students who demonstrate progress through RtI are those who receive private education services, (b) progress monito

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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
Mon May 25 2020
Journal Name
Journal Of Xi'an University Of Architecture & Technology
Iraqi Virtual Science Library (IVSL)): A field study of Iraqi researcher’s viewpoint
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The aim of the research is to shed light on the stages of developing the Iraqi virtual science Library(IVSL) project, and to define its distinctive role in providing all kinds of electronic resources to researchers from professors and graduate students, to identify its contents , the entry interfaces and applications of use, and provide them through electronic portals to publishing houses, research institutions and international universities, The research sample included the teaching staff and researchers participating in educational qualification courses at the Continuing Education Center at the University of Baghdad, The research population and its sample consisted of the category of (IVSL) users, and its sample (387) users. Analysis meth

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