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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
Tue Feb 14 2023
Journal Name
Journal Of Educational And Psychological Researches
Panic Attacks Over COVID 19 : A Survey Study on An Iraqi University Sample
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Abstract

The present paper attempts to detect the level of (COVID-19) pandemic panic attacks among university students, according to gender and stage variables.

To achieve this objective, the present paper adopts the scale set up by (Fathallah et al., 2021), which has been applied electronically to a previous cross-cultural sample consisting of (2285) participants from Arab countries, including Iraq. The scale includes, in its final form, (69) optional items distributed on (6) dimensions:  physical symptoms (13) items, psychological and emotional symptoms (12) items, cognitive and mental symptoms (11) items, social symptoms (8) items, general symptoms (13) items and daily living practices (12) items

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Publication Date
Fri Jan 12 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Are Newly Graduated Pharmacists Competent to Perform Adequately in Hospitals? A Qualitative Study
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Objectives: To assess the qualifications and performance of newly graduated pharmacists and explore factors that affect their performance in public hospitals. Methods: This qualitative study included face-to-face, semi-structured interviews with hospital practitioner pharmacists. It was conducted between March and May 2023 in Kerbala province, Iraq. The participating pharmacists were selected purposefully because they had three or more years of work experience at governmental hospitals. The audio-recording interviews were transcribed. Thematic analyses were used to generate themes and subthemes from the interviews. Results: Twenty-seven hospital pharmacists participated in this study. The study found that there are several factors t

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Publication Date
Thu Nov 30 2023
Journal Name
Iraqi Geological Journal
A Review on Pressure Transient Analysis in Multilayer Reservoir: South Iraq Case Study
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Multilayer reservoirs are currently modeled as a single zone system by averaging the reservoir parameters associated with each reservoir zone. However, this type of modeling is rarely accurate because a single zone system does not account for the fact that each zone's pressure decreases independently. Pressure drop for each zone has an effect on the total output and would result in inter-flow and the premature depletion of one of the zones. Understanding reservoir performance requires a precise estimation of each layer's permeability and skin factor. The Multilayer Transient Analysis is a well-testing technique designed to determine formation properties in more than one layer, and its effectiveness over the past two decades has been

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Publication Date
Wed Mar 01 2023
Journal Name
Baghdad Science Journal
A Study on Co – odd (even) Sum Degree Edge Domination Number in Graphs
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 An edge dominating set    of a graph  is said to be an odd (even) sum degree edge dominating set (osded (esded) - set) of G if the sum of the degree of all edges in X is an odd (even) number. The odd (even) sum degree edge domination number  is the minimum cardinality taken over all odd (even) sum degree edge dominating sets of G and is defined as zero if no such odd (even) sum degree edge dominating set exists in G. In this paper, the odd (even) sum degree domination concept is extended on the co-dominating set E-T of a graph G, where T is an edge dominating set of G.  The corresponding parameters co-odd (even) sum degree edge dominating set, co-odd (even) sum degree edge domination number and co-odd (even) sum degree edge domin

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Publication Date
Fri Jan 01 2021
Journal Name
Brazilian Dental Science
Assessing the level and diagnostic accuracy of osteopontin and oral health status in periodontitis patients with/without Type-2 Diabetes Mellitus
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Publication Date
Fri Jan 01 2021
Journal Name
Brazilian Dental Science
Assessing the level and diagnostic accuracy of osteopontin and oral health status in periodontitis patients with/without Type-2 Diabetes Mellitus
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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Calibrating the Reservoir Model of the Garraf Oil Field
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   History matching is a significant stage in reservoir modeling for evaluating past reservoir performance and predicting future behavior. This paper is primarily focused on the calibration of the dynamic reservoir model for the Meshrif formation, which is the main reservoir in the Garraf oilfield. A full-field reservoir model with 110 producing wells is constructed using a comprehensive dataset that includes geological, pressure-volume-temperature (PVT), and rock property information. The resulting 3D geologic model provides detailed information on water saturation, permeability, porosity, and net thickness to gross thickness for each grid cell, and forms the basis for constructing the dynamic reservoir model. The dynamic reservoir mo

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Publication Date
Mon Oct 04 2923
Journal Name
Journal Of Sustainable Studies
Enantiosemy in a Comparative Aspect: On the Material of Modern Russian and Arabic Languages Энантиосемия в сравнительном аспекте: На материале современного русского и арабского языков التضاد - دراسة مقارنة : اللغات الروسية والعربية الحذيثة أنمورجا
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This work is devoted to a comparative study of the phenomenon of enantiosemy in Russian and Arabic.Everyone knows the term antonyms - words of the same part of speech, opposite in meaning, such as: Day and night, white and black, truth and lies. But in Russian, Arabic and other languages there is an interesting phenomenon, which consists in the fact that one word has two opposite meanings. Such a phenomenon in linguistics is called enantiosemy (from the Greek words enantios - "opposite" and sema - "sign")

Publication Date
Tue Jan 01 2013
Journal Name
International Journal Of Advances In Pharmacy, Biology And Chemistry
Synthesis of NSAID with Sulfonamide Conjugates as Possible Mutual Prodrugs using Amino Acid Spacer
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The purpose of this research work is to synthesize conjugates of NSAIDs (ibuprofen, and naproxen) with sulfadiazine as possible mutual prodrugs to overcome the local gastric irritation of NSAIDs with free carboxyl group by formation of ester linkage that supposed to remain intact in stomach and may hydrolyze in intestine chemically or enzymatically; in addition to that attempting to target the synthesized derivative to the colon by formation of azo bond that undergo reduction only by colonic bacterial azoreductaze enzyme to liberate the parent compound to act locally (treatment of inflammation and infections in colon)

Publication Date
Tue Jun 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Improving Treatment Performance of Dissolved Air Flotation System by Using Ionic Liquids as Surfactants
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The effect of three ionic liquids viz., 1-hexyl-3-methylimidazolium tetrafluoroborate (ILE), 1-hexyl-3-metylimidazolium hexafluorophosphate (ILF) and 1-octyl-3-methylimidazolium tetrafluoroborate (ILG) when used as surfactants on the performance of dissolved air floatation (DAF) was investigated.

   Experiments were conducted at a temperature of 30-35 ºC, 10ppm ferric chloride as coagulant, 50% recycle ratio, pH 8, and 10 minutes treatment time  to find oil and grease (OG) and turbidity removal efficiencies at saturation pressure (2-6) bar.

ILs were used at concentration of 50 µl/liter of treated water in two positions in DAF system; the saturation vessel and the treatment tank. The performance using ILs

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