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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
Wed Jan 13 2021
Journal Name
Egyptian Journal Of Chemistry
Development of a nanostructured double-layer coated tablet based on polyethylene glycol/gelatin as a platform for hydrophobic molecules delivery
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The aim of the current study was to develop a nanostructured double-layer for hydrophobic molecules delivery system. The developed double-layer consisted of polyethylene glycol-based polymeric (PEG) followed by gelatin sub coating of the core hydrophobic molecules containing sodium citrate. The polymeric composition ratio of PEG and the amount of the sub coating gelatin were optimized using the two-level fractional method. The nanoparticles were characterized using AFM and FT-IR techniques. The size of these nano capsules was in the range of 39-76 nm depending on drug loading concentration. The drug was effectively loaded into PEG-Gelatin nanoparticles (≈47%). The hydrophobic molecules-release characteristics in terms of controlled-releas

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Publication Date
Sun May 05 2024
Journal Name
Review Of Clinical Pharmacology And Pharmacokinetics - International Edition
Comparative evaluation of pharmacokinetic parameters between a pure nisoldipine suspension and a nisoldipine-loaded bilosome suspension
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Bilosomes are nanocarriers that contain bile salts in their vesicular bilayer, thereby enhancing their flexibility and durability in the gastrointestinal tract. Unlike conventional vesicular systems they provide distinct advantages such as streamlined manufacturing procedures, cost efficiency, and improved stability. The main objective of this study was to attain a comparison of the pharmacokinetic parameters of nisoldipine (NSD) after administering an ordinary NSD suspension and an NSD-loaded bilosome suspension. The study used 60 Swiss albino rats weighing 200±15 g and divided into two groups (n=30 each). A dose of 2.2 mg/kg of NSD was administered from the ordinary NSD suspension to the rats of the first group and the same dose

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Publication Date
Fri Jan 01 2016
Journal Name
Arpn Journal Of Engineering And Applied Sciences
Implementation And Evaluation Of Apm 2.6 - Controlled Quadcopter With Aerial Imagery As A Case Study
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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Engineering
Estimation of Water and Energy Saving by Rainwater Harvesting: Sulaimani City as a Case Study
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Rainwater harvesting could be a possible solution to decrease the consequences of water scarcity and energy deficiency in Iraq and the Kurdistan Region of Iraq (KRI). This study aims to calculate the water and energy (electricity) saved by rainwater harvesting for rooftops and green areas in Sulaimani city, KR, Iraq. Various data were acquired from different formal entities in Sulaimani city. Moreover, Google Earth and ArcMap 10.4 software were used for digitizing and calculating the total rooftop and green areas. The results showed that for the used runoff coefficients (0.8 and 0.95), the harvested rainwater volumes were 2901563 and 12197131 m³ during the study period (2005 – 2006) and (2019-2020). Moreover, by compa

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Publication Date
Mon Feb 08 2021
Journal Name
Public Works Management & Policy
Causes of Problems in Post-Disaster Emergency Re-Construction Projects—Iraq as a Case Study
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This study examines the causes of time delays and cost overruns in a selection of thirty post-disaster reconstruction projects in Iraq. Although delay factors have been studied in many countries and contexts, little data exists from countries under the conditions characterizing Iraq during the last 10-15 years. A case study approach was used, with thirty construction projects of different types and sizes selected from the Baghdad region. Project data was gathered from a survey which was used to build statistical relationships between time and cost delay ratios and delay factors in post disaster projects. The most important delay factors identified were contractor failure, redesigning of designs/plans and change orders, security is

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Publication Date
Sat Oct 31 2020
Journal Name
Eastern-european Journal Of Enterprise Technologies
Design and development of high-accuracy machine for wire bending
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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of The College Of Languages (jcl)
Dylan Thomas:The Vision of Death as a Prologue to a New Life
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Dylan Thomas (1914-1953) is a modern poet belongs to the apocalyptic movement of the 1940's.This movement is influenced by the doctrines and techniques of surrealism.

              Poetry for him should not be primarily concerned with man in society, but with the celebration of spiritual truth. It should bring to light the hidden causes, hence  his personal interest is to strip darkness and explore the inward motives. To do this he uses a cluster of images: a constant building up and breaking down of images. His poetry depends on the romantic spontaneity, suggestiveness of the Symbolists and the the surrealists' mysterious liberation of the unconsciousness and

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of The College Of Languages
Dylan Thomas:The vision of Death as a Prologue to a New Life
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Dylan Thomas (1914-1953) is a modern poet belongs to the apocalyptic movement of the 1940's.This movement is influenced by the doctrines and techniques of surrealism. Poetry for him should not be primarily concerned with man in society, but with the celebration of spiritual truth. It should bring to light the hidden causes, hence his personal interest is to strip darkness and explore the inward motives. To do this he uses a cluster of images: a constant building up and breaking down of images. His poetry depends on the romantic spontaneity, suggestiveness of the Symbolists and the the surrealists' mysterious liberation of the unconsciousness and the emotional involvement in the dynamics of life. In "Light Breaks

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Publication Date
Wed Jan 30 2013
Journal Name
Al-kindy College Medical Journal
Using the Abbreviated Version of Modification of Diet in Renal Disease Formula as A Primary Estimate for the Prevalence of Undiagnosed Chronic Kidney Disease in Patients with Acute Stroke
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Introduction: The association between acute stroke and
renal function is well known. The aim of this study is to
know which group of patients with acute stroke is more
likely to have undiagnosed Chronic Kidney Disease and
which risk factors are more likely to be associated with.
Methods:We studied 77 patients who were diagnosed to
have an acute stroke.Patients were selected between
April2011andJune 2011 using the " 4-variable
Modification of
Diet in Renal Disease Formula " which estimates
Glomerular Filtration Rate using four variables :serum
creatinine ,age ,race and gender.
Results :The study included 38 male and 39 females
patients ,aged (35-95) years. Glomerular Filtration Rate in
patients wi

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Publication Date
Sat Feb 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation The Performance efficiency of the general company for lather Industries (a practical study)
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The performa of evaluation process is a process that should be carried out by all industrial management in order to stand on aspects of development or underdevelopment of the various departments and activities in its industrial project for the purpose of identifying obstacles and find out the causes and then avoid them quickly. And intended to rectify the performance evaluation of the  activities of  industrial project  or economic union by measuring the results achieved within a specific operational process and compare it to what is already targeted, and often the time for comparison of one year.

The process of performance evaluation depends upon several criteria and indicators within the

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