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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 May 12 2025
Journal Name
The International Journal Of The History Of Sport
Exploring Sport’s Role in Mitigating Conflicts Gulf Cup as a Case Study
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Conflict, peace, and sports have a long history as practical realities, and their correlation has become an important subject of study in the last decades of the twentieth century. Sport has infiltrated peace and conflict studies as a tool for resolving conflict and building peace, but opinions have differed between those who say it is a positive tool and others who see it as negative. The Gulf Cup is one of the champions that have never been studied, and in-depth research about it has not been done. This tournament has affected the relations between the states involved. The politics cast its shadow on the Gulf Cup. The paper aims to shed light on how political events in the region have consistently affected the Gulf Cup and how politics in

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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of Artificial Accelerated Aging on The Color of Ceramic Veneers Cemented With Different Resin Cements (A Comparative In Vitro Study)
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ABSTRACT Background: Color changes that are detectable to human eye can affect the esthetic appearance of ceramic veneers. The purpose of this study was to evaluate and compare the effect of artificial accelerated aging on the color of ceramic veneers cemented with different resin cements. Materials and Methods: Sixty discs were prepared with 0.5 mm thickness, 30 discs made from IPS e.max press (Ivoclar Vivadent) and 30 discs were made from VITA Enamic (VITA Zahnfabrik). The discs were cemented with three resin cements: Variolink Veneer MV 0 shade (Ivoclar Vivadent), Rely X veneer Translucent shade (3M ESPE) and NX3 Nexus Clear shade (Kerr Corporation) with 0.1 mm thickness. The spectrophotometer Easyshade Advance was used to measure the co

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Publication Date
Sun Jan 02 2022
Journal Name
Neuroquantology
Treatment of primary trigeminal neuralgia: A comparative study of microvascular decompression surgery and stereotactic gamma knife radiosurgery
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Objectives To compare the clinical efficacy of microvascular decompression surgery (MVD) and gamma knife radiosurgery (GKR) as a treatment for patients with primary trigeminal neuralgia (TN) and evaluate the outcome regarding pain relief, recurrence, and complications with both modalities of treatment. Patients and Methods A randomized prospective study conducted in SaadAlwitry Neurosciences Hospital, Baghdad, Iraq. Eighty-four patients with TN from January 2016 to January 2018, 45 patients had GKR while 39 patients treated with MVD. The pain evaluated pre-and post-operatively using the Barrow Neurological Institute Pain Intensity scale (BNIPI), visual analog scale (VAS) and Brief Pain Inventory Facial (BPI-Facial) scoring systems. In GKR p

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Publication Date
Mon Sep 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparative Study of the Influence of Different Types of Polymers on Viscosity Index and Pour Point of Iraqi Base Oils
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In this study, the effects of blending the un-branched acrylate polymer known as Poly (n-decyl acrylate), and the branched acrylate polymer known as Poly (iso-octyl acrylate), on the viscosity index (VI), and the pour point of the Iraqi base stocks 40, and 60 respectively, were investigated. Toluene was used as a carrier solvent for both polymer types. The improvement level of oils (VI, & pour point) gained by blending the oil with the acrylate derived polymers was compared with the values of (VI, and pour point) gained by blending the oil with a commercial viscosity index, and pour point improver. The commercial lubricant additive was purchased and used by Al-Daura Refineries. It consisted of an un-known olefin copolymer dissolved i

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Publication Date
Thu Oct 01 2009
Journal Name
Jssdds
Topical 10% lactic acid solution in the treatment of pityriasis versicolor in comparison with topical 1% clotrimazol solution (single-blind, comparative and therapeutic study)
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KE Sharquie, AA Noaimi, AM Oweid, JSSDDS, 2009 - Cited by 2

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Enhancement of Episiotomy Healing Using (790-805) nm Diode Laser as a Supplementary Treatment
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To show the impact of 790-805 nm diode laser irradiations on wound healing as a supplementary treatment in women underwent episiotomies, and to assess the laser parameters that were used .Material and methods: Eighteen female patients were included in this study; all of them underwent mediolateral episiotomy. Ten patients received laser therapy- diode laser (K Laser) (790-805) nm in CW mode of operation (and eight patients were the control group. Spot size of 8mm, time for exposure for each spot was 30 seconds. The power used was 0.6 W .The power density for each spot of treatment was 1.19 W/cm2 per session (non contact mode of application of laser therapy).The group studied received 2 sessions of laser radiation, day 4, and day 8 after

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Publication Date
Sun Jun 21 2020
Journal Name
Baghdad Science Journal
Synthesis of Carbon Nano Rods from Plastic Waste (PP) Using MgO AS A Catalyst
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    In this research, CNRs have been synthesized using pyrolysis of plastic waste(pp) at 1000 ° C for one hour in a closed reactor made from stainless steel, using magnesium oxide (MgO) as a catalyst. The resultant carbon nano rods were purified and characterized using energy dispersive X-ray spectroscopy (EDX), X-ray powder diffraction (XRD). The surface characteristics of carbon rods were observed with the Field emission scanning electron microscopy (FESEM). The carbon was evenly spread and had the highest concentration from SEM-EDX characterization. The results of XRD and FESEM have shown that carbon Nano rods (CNRs) were present in Nano figures, synthesized at 1000 ° C and with pyrolysis temperature 400° C. One of t

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Publication Date
Wed Mar 25 2020
Journal Name
International Journal Of Drug Delivery Technology
Study of Molecular Interaction for Antibiotic Drug with Sugar Solutions at Different Temperature
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The interactions of drug amoxicillin with maltose or galactose solutions with a variation of temperature have been discussed by taking in the volumetric and viscometric procedures. Physical properties [densities (ρ) and viscosities (η)] of amoxicillin (AMOX) aqueous solutions and aqueous solutions of two type saccharides (maltose and galactose 0.05m) have been measured at T = (298.15, 303.15 and 308.15) K under atmospheric pressure. The apparent molar volume (ϕv cm3mole-1) has been evaluated from density data and fitted to a Redlich-Mayer equation. The empirical parameters of the Mayer-Redlich equation and apparent molar volume at infinite dilution ذv were explicated in terms of interactions from type solute-solvent and solute

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Publication Date
Sat May 08 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Sequencing of IL-10 Gene Promoter for -592 (A/C) and -1082 (A/G) Positions in Iraqi Children Patients with Type 1 Diabetes Mellitus
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We studied the relationship between DNA sequencing of interleukin-10 (IL-10) gene promoter for -1082 (A/G) and -592 (A/C) positions with the concentration of IL-10 in blood serum of Iraqi children with type 1 diabetes mellitus (T1D). Fifty blood serum samples collected from children with age ranged between 7-12 years. Thirty-five blood samples collected from patient children with T1D, and compared with 15 healthy children age matched as control sample. The results revealed decreasing in anti-inflammatory IL-10 concentration in T1D patient’s blood serum (0.068 Pg/ml) as compared with the control sample (0.111 Pg/ml). No significant differences were found in interleukin concentration between the studied samples when they analyzed with the M

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Publication Date
Sun Mar 01 2020
Journal Name
Journal Of Engineering
Study the Effect of Particle Sizes and Concentration on the Rheological Properties of Iraqi Bentonite for Using as Drilling Fluids
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The aim of this study is to identify the effect of particle size and to increase the concentration of Iraqi bentonite on rheological properties in order to evaluate its performance and to know if it can be used as drilling fluid without additives or not. In this study, Iraqi bentonite was carried out by mineral composition (XRD), chemical composition (XRF) and Particle size distribution (PSD), and its rheological properties were measured at different particle size and concentration. The results showed that when the particle size of Iraqi bentonite decreased, and the rheological properties were increased with increased concentration of Iraqi bentonite. Also, Iraqi bentonite was unable to use as drilling fluid without certain additives.

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