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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 Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Potential Positive Effects using Coenzyme Q10 Supplement as Adjuvant Therapy to Gabapentin for Managing Diabetic Neuropathy
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The most prevalent chronic complication of diabetes mellitus is diabetic neuropathy. The pathogenesis of diabetic neuropathy is exacerbated by hyperglycemia-induced oxidative stress, which causes nerves to deteriorate in a programmed manner. Many clinical trials depend on supplement in an attempt to improve neuropathy symptoms such as (pain & tingling) and patient quality of life, one of them is Coenzyme Q10 which is reported to have an anti-inflammatory and antioxidant effects, and was totally nontoxic and non-reported side effects. This study aimed to evaluate using a Coenzyme Q10 supplement as an adjuvant therapy to gabapentin to improve the clinical symptoms of diabetic neuropathy in relation to its anti-inflammatory and antioxid

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Publication Date
Fri Nov 01 2019
Journal Name
Civil Engineering Journal
Time-Cost-Quality Trade-off Model for Optimal Pile Type Selection Using Discrete Particle Swarm Optimization Algorithm
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The cost of pile foundations is part of the super structure cost, and it became necessary to reduce this cost by studying the pile types then decision-making in the selection of the optimal pile type in terms of cost and time of production and quality .So The main objective of this study is to solve the time–cost–quality trade-off (TCQT) problem by finding an optimal pile type with the target of "minimizing" cost and time while "maximizing" quality. There are many types In the world of piles but  in this paper, the researcher proposed five pile types, one of them is not a traditional, and   developed a model for the problem and then employed particle swarm optimization (PSO) algorithm, as one of evolutionary algorithms with t

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Publication Date
Sat Aug 01 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
Building and legalizing a test for evaluating the tactical learning of the footwork for the foil fencer in the fencing game
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AA wahid, journal mustansiriyah of sports science, 2023

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Publication Date
Wed Jun 13 2012
Journal Name
Journal Of Kerbala University
Thermo physical behaviour of binary and ternary systems for cyclohexanol with some Ketones at three temperature
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Publication Date
Wed Dec 01 2010
Journal Name
Al-khwarizmi Engineering Journal
Prediction of Equilibrium Mixing Index and Optimum Mixing Time for Three solid materials in Fluidized Column
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     Equilibrium and rate of mixing of free flowing solid materials are found using gas fluidized bed. The solid materials were sand (size 0.7 mm), sugar (size0.7 mm) and 15% cast iron used as a tracer. The fluidizing gas was air with velocity ranged from 0.45-0.65 m/s while the mixing time was up to 10 minutes. The mixing index for each experiment was calculated by averaging the results of 10 samples taken from different radial and axial positions in fluidized QVF column 150 mm ID and 900 mm height.

     The experimental results were used in solving a mathematical model of mixing rate and mixing index at an equilibrium proposed by Rose. The results show that mixing index increases with inc

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Publication Date
Mon Jul 01 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
Study the Effect of Cyperus Rotundus Extracted as Mouthwash on the Corrosion of Dental Amalgam
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Many extracted material were used as mouthwash to settle different kinds of oral fungi and bacteria. In this study an extractive of Cyperus rotundus plant E.C.R. which is very active as a mouthwash, was used in concentration range (10-25) ppm in artificial saliva at pH=6.4 and temperature range (288-318) K, to study it’s inhibitory effect on the corrosion of dental amalgam. Potentiostatic and cyclic polarization were used to follow this study. The presence of E.C.R. lead to shift the corrosion potential to the active direction and decreased the corrosion rate to about 98.87%, the inhibition action of E.C.R. resulting from the adsorption of C.R.E. layer between amalgam and saliva as FTIR spectrums shows, where the variety of FTIR adsorptio

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Publication Date
Mon Jan 02 2023
Journal Name
Res Militaris
Rehabilitation program for treatment Tennis Elbow (Lateral Epicondylalgia) suffered by the players of Al-Rafidain Sports Club for Tennis League three players in Diyala province
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Abstract Lateral Epicondylitis (LE) which has been referred to as the Tennis Elbow as well is a lesion affecting common tendinous origins of wrist extensors due to chronic overuse injury that results in damaging common extensor tendons which join forearm extensor muscles to humerus. The aim of the present evidence-based clinical statement is reviewing scientific evidences for efficacy of a variety of the rehabilitation methods, chronic lateral epicondylitis management. It is focused upon treating chronic lateral epicondylitis and the latest developments in physiotherapy area for managing chronic lateral epicondylitis. Due to the fact that primary physical impairments in the LE are decreased is the strength of the grip, fundamentally due to

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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
The American Occupation Policy toward Japan 1945-1951 and Iraq 2003-2008: Comparative Historical Study
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With their strategic and geographical positions, Japan and Iraq are one of the major
countries in the world, especially to the United States. Japan lies near the two American
Continents, separated only by the Pacific and it is only normal to have the interests of both
countries crossed and joined in the Far East region. This made the occupation of Japan an
inventible matter in the second half of the 20th century. Iraq, on the other hand, has strategic
position in the Middle East, being surrounded by many active countries like Turkey, Iran, and
Gulf countries, besides Iraq’s oil wealth which is needed by such industrial country like the
United States.

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Publication Date
Wed Aug 02 2023
Journal Name
Bionatura
Comparative Study of IgG Between Iraqi Covid-19 Patients and Vaccinated Individuals
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COVID-19 is a coronavirus disease caused by the severe acute respiratory syndrome. According to the World Health Organization (WHO), coronavirus-2 (SARS-CoV-2) was responsible for 87,747,940 recorded infections and 1,891,352 confirmed deaths as of January 9, 2021. Antibodies that target the Sprotein are efficient in neutralizing the virus. Methodology: 180 samples were collected from clinical sources (Blood and Nasopharyngeal swabs) and from different ages and genders at diverse hospitals in Baghdad / IRAQ between November 5, 2021, to January 20, 2022. All samples were confirmed infected with COVID-19 disease by RT-PCR technique. Haematology analysis and blood group were done for all samples, and Enzyme-Linked Immunosorbent Assay used an Ig

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Publication Date
Mon Jan 01 2024
Journal Name
Iranian Journal Of Veterinary Medicine
Comparative Study of Bacterial Contamination in Local Iraqi Sheep and Goats Semen
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Background: Semen contamination is a detrimental factor in decreasing fertility. Seasonal changes may affect the contamination, too. Objectives: This study was designed to detect semen contamination in ovine and caprine during different seasons. Methods: Six fully mature male sheep and goats were subjected to electro-ejaculator collection twice monthly from February 1, 2022, to January 31, 2023 (Spring, February 1, 2022-April 30, 2022; Summer, May 1, 2022, July 31, 2022; Autumn August 1, 2022, October 31, 2022; Winter November 1, 2022, January 31, 2023), for studying the seasonal effect. A total of 288 semen samples were collected from both species (36 samples from each per season). All samples were subjected to bacterial isolatio

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