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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
Mon Jan 01 2024
Journal Name
Malaysian Journal Of Nursing
Experiences of Nurses in Providing Care for Patients on the Cancer Journey: A Cross-Sectional Survey
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Publication Date
Thu Apr 03 2025
Journal Name
Journal Of The American Oil Chemists' Society
A novel deep eutectic solvent‐based liquid membrane for the extraction of glycerol from crude biodiesel
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Abstract<p>This study used deep eutectic solvent (DES) as the liquid membrane in a bulk liquid membrane system (BLM) to remove glycerol from waste cooking oil‐based biodiesel. The DES was prepared from choline chloride and tetraethylene glycol at a molar ratio of 1:5. Diethyl ether was employed as a novel strip phase for the glycerol in BLM. The effects of the DES: biodiesel ratio, stirring speed, and extraction time on the extraction and stripping efficiencies were investigated. The results showed that BLM could give better glycerol removal from biodiesel than mechanical shaking. Increasing the DES: biodiesel ratio, stirring speed, and extraction time can enhance glycerol removal from the feed phase, achievi</p> ... Show More
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Publication Date
Wed Feb 25 2026
Journal Name
Journal Of Physical Education
Analytical – Comparative Study of Some Kinematical Variables Of Jump Shot and Shooting in Youth Basketball Players
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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Between the Methods Estimate Nonparametric and Semiparametric Transfer Function Model in Time Series Using Simulation
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Publication Date
Thu Dec 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of serum levels of monocyte chemoattractant protein 1 (MCP 1) in patients with periodontitis and atherosclerotic cardiovascular disease
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Background: Monocyte chemotactic protein-1 (MCP-1) is a chemokine expressed by inflammatory and endothelial cells. It has a crucial role in initiating, regulating, and mobilizing monocytes to active sites of periodontal inflammation. Its expression is also elevated in response to pro-inflammatory stimuli and tissue injury, both of which are linked to atherosclerotic lesions. Aim of the study: To determine the serum level of MCP-1 in patients with periodontitis and atherosclerotic cardiovascular disease in comparison to healthy control and evaluate the biomarker's correlations with periodontal parameters. methods: This study enrolled 88 subjects, both males and females, ranging in age from 36-66 years old, and divided into four groups: 1<

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Publication Date
Wed Jan 01 2020
Journal Name
Research Journal Of Pharmacy And Technology
The effectiveness of topical vitamin k cream 1% in the treatment of steroid-induced rosacea
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Publication Date
Wed Feb 25 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of MMP9, as a marker of local invasion in Hodgkin’s and Non-Hodgkin’s lymphoma of the head and neck region
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Background: Malignant lymphoma is the generic term given to tumors of the lymphoid system and specifically of lymphocytes and their precursor cells, While all lymphomas are malignant neoplasms, there is a wide spectrum of clinical behavior, with some following an indolent clinical course and others behaving in an aggressive manner (will causing death in a short time frame if left untreated). The metastatic process involves intravasation and extravasation of tumor cells, followed by reimplantation of tumor cells, formation of a new tumor stoma, Degradation of the extracellular matrix and components of the basement membrane by proteases facilitates the detachment of tumor cells, their crossing of tissue boundaries, and invasion into adjacent

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Three Dimensional MHD Simulationof Comet Hale-Bopp Tail
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The interaction between comet Hale-Bopp tail with the solar wind is investigated in the present paper using magneto-hydrodynamic (MHD) numerical simulation, which accounts for the presence of the interplanetary magnetic field (IMF). The simulation is based on three-dimensional Lax-Wendroff explicit scheme, providing second-order accuracy in space and time. The ions produced from the nucleus of the comet will add considerable effects on the microstructure of the solar wind, thus severely altering its physical properties. The present simulation focuses on careful analysis of these properties by means of simulating the behavior of the comet Hale-Bopp’s tail at 1 AU from the sun. These properties include the changes of the plasma density,

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Publication Date
Sun Dec 03 2017
Journal Name
Baghdad Science Journal
A Study of Zooplankton Community in Dukan Lake, Kurdistan Region-Iraq, with a New Record of Craspedacusta sowerbii Lankester (1880) Medusa (Cnidaria: Hydrozoa)
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A study of Zooplankton community has been carried out at four selected sites on Dukan Lake. Samples of water and zooplankton were collected monthly for the period from July 2015 to February 2016. Some physical and chemical properties of water were studied and the results showed that the air temperature were ranged from 0 to 36.16 °C, water temperature ranged from 2.83 to 34.66 °C, hydrogen ion concentration of studied sites were found to lie in alkaline side, it was ranged between 6.87 to 8.57, electrical conductivity ranged from 190.79 to 850.08 µs.cm­¹, turbidity ranged from 0.9-7.7 NTU, and dissolved oxygen from 3.3 to 6.8 mg.l-¹ while BOD5 were ranged from 0.53 to 34.66 mg.l-¹. Concerning to the zooplankton, 37 species were ident

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Publication Date
Fri Jan 05 2024
Journal Name
Al-academy
Characteristics Of The Place In Contemporary Iraqi Television Drama Serial Iraqi love And Peace Model ( Analytical Study )
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Filled the place thought philosophers and ancient is the identity that you know The value of belonging to a World Geography existential - the spiritual , and Which is characterized by the structure humanity from one another and the Rest of the organisms they interact with him alone by environmental Conditions - surrounding has to achieve time through continuous movement Localized or comprehensive . The place is exemplified by making special Natural Great Creator, I believe making structure humanity combined - Individual interactive because of its influential role in all daily consumer Productions and creative arts, specifically drama's TV , because the place in Aesthetic discourse - TV drama directly affect the creating and building the

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