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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 31 2011
Journal Name
Al-khwarizmi Engineering Journal
Effect of Mixed Corrosion Inhibitors in Cooling Water System
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The effect of mixed corrosion inhibitors in cooling system was evaluated by using carbon steel specimens and weight loss analysis. The carbon steel specimens immersed in mixture of sodium phosphate (Na2 HPO4) used as corrosion inhibitor and sodium glocunate (C6 H11 NaO7) as a scale dispersant at different concentrations (20,40, 60, 80 ppm) and at different temperature (25,50,75 and 100)ºC for (1-5) days. The corrosion inhibitors efficiency was calculated by using uninhibited and inhibited water to give 98.1%. The result of these investigations indicate that the corrosion rate decreases with the increase the corrosion inhibitors concentration at 80 ppm and at 100ºC for 5 days, (i.e,

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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
A Unit Plan Based Upon The MI Theory: A theoretical study with an application Inside The Classroom
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This research basically gives an introduction about the multiple intelligence
theory and its implication into the classroom. It presents a unit plan based upon the
MI theory followed by a report which explains the application of the plan by the
researcher on the first class student of computer department in college of sciences/
University of Al-Mustansiryia and the teacher's and the students' reaction to it.
The research starts with a short introduction about the MI theory is a great
theory that could help students to learn better in a relaxed learning situation. It is
presented by Howard Gardener first when he published his book "Frames of
Minds" in 1983 in which he describes how the brain has multiple intelligen

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Publication Date
Wed Jan 01 2014
Journal Name
International Journal Of Computer Applications
Mobile Position Estimation based on Three Angles of Arrival using an Interpolative Neural Network
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In this paper, the memorization capability of a multilayer interpolative neural network is exploited to estimate a mobile position based on three angles of arrival. The neural network is trained with ideal angles-position patterns distributed uniformly throughout the region. This approach is compared with two other analytical methods, the average-position method which relies on finding the average position of the vertices of the uncertainty triangular region and the optimal position method which relies on finding the nearest ideal angles-position pattern to the measured angles. Simulation results based on estimations of the mobile position of particles moving along a nonlinear path show that the interpolative neural network approach outperf

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Publication Date
Mon Jan 26 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Force decay of orthodontic elastomeric chains by using three different mechanisms simulating canine retraction
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Background: The ideal force-delivery system must: provide optimal tooth moving forces that elicit the desired effects, be comfortable and hygienic for the patient, require minimal operator manipulation and patient cooperation and provide rapid tooth movement with minimal mobility during orthodontic therapy, the elastomeric chains have the greatest potential to fulfill these requirements. Materials and Methods: This in vitro study was designed to determine the effect of three different mechanisms for canine retraction : (6-3 , 6-5-3 and chain loop ) on the load relaxation behavior of three types of elastomeric chains : (maximum clear , maximum silver and extreme silver) from the same company (Ortho Technology company) with two different bran

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Publication Date
Sat Apr 30 2022
Journal Name
Al-kindy College Medical Journal
Safety profile of immediate post-partum intrauterine device insertion during caesarean delivery – a clinical trial with three years of follow up
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Background Many countries recommend the use of long-acting reversible contraceptive intrauterine device immediately after cesarean delivery. The cesarean delivery rate in Iraqi public hospitals is 32.2% and may reach 85.8% in private hospitals. Immediate post-partum intrauterine device insertion at cesarean is rarely done in Iraq. Objectives To assess the safety and practicality of immediate post-partum intrauterine device insertion during cesarean delivery for family planning and pregnancy spacing in Iraqi women. Subjects and Methods A single arm clinical trial included 150 eligible women who attended Al-‎Elwiyah Maternity Teaching Hospital or Al Hayat Rahibat Hospital for term delivery. A copper intrauterine device was placed in the ute

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Publication Date
Tue Dec 15 2020
Journal Name
Journal Of Pharmaceutical And Biological Sciences
Fascinating approach for using metabolites products of living microorganisms as reducing agents for preparing silver nanoparticles
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A crucial area of research in nanotechnology is the formation of environmentally benign nanoparticles. Both unicellular and multicellular play an important role in synthesis nanoparticles through the production of inorganic materials either intracellularly or extracellularly. The agents (pigments, siderophores, cell extracted metabolites and reducing compounds) were used to prepare silver nanparticles with different sizes and shapes. The color variations (dark yellow, slightly dark yellow and golden yellow) arising from changes in the composition, size, and shape of nanoparticles, surrounding medium can be monitored using UV-visible spectrophotometer. These effects are due to the phenomena called surface plasmon resonance. The silver nanopa

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The dropping of three zeroes from Iraqi dinar
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           The purpose of this research is to explain the effect of the dropping of three zeroes from Iraqi dinar on the basic role of the dinar and derivative and dynamic in transaction of Iraqi economic. the importance of this research comes from the effect of this operation on the evaluation of the exchange between the individuals of Iraqi society and the other between the Iraqi individuals and the foreign whom use the Iraqi dinar as a tool for exchange also the effect of the operation on the reserves of the Iraqi dinar the results of this research are as the following:-

1-the operation of dropping of zeroes must be associated with increase of the sharing of economic sectors wi

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Publication Date
Thu Jul 01 2010
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
SEDIMENTO LOGICAL STUDY OF SHIRANISH FORMATION WELL DD-1 (N-IRAQ)
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Shiranish formation has been divided into two microfacies units: 1-Marly biowacke stone facies 2-Biogenic pack stone facies These microfacies reflected marine deep shelf margin in the upper part of the formation, the lower part was deeper. 238 slides were investigated depending on Mineralogical, compositional and Biological processes, which reflect deep shelf margin at upper part of the formation, but at the lower part open sea environment. The age of the formation is estimated depending on the recognized biostratigraphic zone using the index fossils to be Upper- Middle Maestrichtian.

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation of a New Dosage Form of Metoclopramide Hydrochloride as Orodispersible Tablet
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Metoclopramide HCl (MTB) is a potent antiemetic drug used for the treatment of nausea and vomiting. Many trials were made to prepare a satisfactory MTB orodispersible tablet using direct compression method.Various super disintegrants were used in this study which are croscarmellose sodium (CCS), sodium starch glycolate (SSG) and crospovidone (CP). The latter was the best in terms of showing the fastest disintegration time in the mouth.Among the different diluents utilized, it was found that a combination of microcrystalline cellulose PH101 (MCC 101), mannitol, dicalcium phosphate dihydrate (DPD) and Glycine was the best in preparing MTB orodispersible tablet with fastest disintegration time in the mouth.The physical parameters of the pre

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Publication Date
Wed Nov 30 2022
Journal Name
Iraqi Journal Of Science
Synthesis and Characterization of Ni2O3 as a Phase of Nickel Oxide Nanomaterial
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    Ni2O3 nanomaterial, a phase of nickel oxide, is synthesized by a simple chemical process. The pure raw materials used in the present process were nickel chloride hexahydrate NiCl2.6H2O and potassium hydroxide KOH by utilizing temperature at 250 oC for 2 hour.  The structural, morphological and optical properties of the synthesized specimens of Ni2O3 were investigated employing diverse techniques such as XRD, AFM, SEM and UV-Vis, respectively. The XRD technique confirms the presence of Ni2O3 nanomaterial with crystal size of 57.083 nm which indexing to the (2θ) of 31.82; this results revealed the Ni2O3 was a phase of nickel oxide with Nano structure. The synthesized Ni2O3 will be useful in manufacturng electrodes materials f

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