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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
Thu Dec 30 2021
Journal Name
Diyala Agricultural Sciences Journal
A Study of Some Biological Aspects of Pacu Piaractus Brachypomus (G. Cuvier, 1818)
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The present study attempts to shed light on some biological aspects and characteristics of Piaractus brachypomus, including some biometrics, phenotypic and feeding pattern that characterizes this species. Besides, the study touches upon the body shape and the Otolith. These fish species have recently been seen frozen in the Iraqi local market. The standard length of fish specimens in this study reach 26.55cm it exceeded the specimens of Pacu fish collected from other studies from other countries, As well the specimens weight was 632gm it exceeded other studies mentioned in this manuscript. As the irregularity in the distribution of teeth rows, especially in the lower jaw was clear in our specimens. The average weight of some skull b

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Petroleum Research And Studies
A Numerical Study of Tertiary Oil Recovery by Injection of Low-Salinity Water
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The injection of Low Salinity Water (LSWI) as an Enhanced Oil Recovery (EOR) method has recently attracted a lot of attention. Extensive research has been conducted to investigate and identify the positive effects of LSWI on oil recovery. In order to demonstrate the impact of introducing low salinity water into a reservoir, simulations on the ECLIPSE 100 simulator are being done in this work. To simulate an actual reservoir, an easy static model was made. In order to replicate the effects of injecting low salinity water and normal salinity, or seawater, the reservoir is three-phase with oil, gas, and water. It has one injector and one producer. Five cases were suggested to investigate the effect of low salinity water injection with differen

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Publication Date
Sat Apr 01 2023
Journal Name
Siriraj Medical Journal
The Potential of Vitamin-D-Binding Protein as a Urinary Biomarker to Distinguish Steroid-Resistant from Steroid-Sensitive Idiopathic Nephrotic Syndrome in Iraqi Children
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Objective: To determine the ability of uVDBP to discern SRNS from steroid-sensitive nephrotic syndrome (SSNS) in Iraqi children. Materials and Methods: This cross-sectional study enrolled children with SRNS (n=31) and SSNS (n=32) from the pediatric nephrology clinic of Babylon Hospital for Maternity and Pediatrics over three months. Patients' characteristics in terms of demographics, clinical data, and urinary investigations were collected. Quantitative analysis of uVDBP levels was undertaken via a commercially available ELISA kit. Results: The median uVDBP values were significantly higher (p-value<0.001) in the SRNS group (median=10.26, IQR=5.91 μg/mL) than in the SSNS group (median=0.953, IQR=4.12 μg/mL). A negative correlati

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Publication Date
Mon Jan 01 2024
Journal Name
The International Journal Of Central Banking
USING SOME NONPARAMETRIC ESTIMATORS OF THE ERROR CORRECTION MODEL TO MEASURE THE EFFECT OF CHANGES IN BANK DEPOSITS ON THE MONEY SUPPLY
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In this paper, the effect of changes in bank deposits on the money supply in Iraq was studied by estimating the error correction model (ECM) for monthly time series data for the period (2010-2015) . The Philips Perron was used to test the stationarity and also we used Engle and Granger to test the cointegration . we used cubic spline and local polynomial estimator to estimate regression function .The result show that local polynomial was better than cubic spline with the first level of cointegration.

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
Utilizing Artificial Intelligence Tools in Enhancing Training of Trainers (ToT) Programs: Modern Approaches and Practical Applications
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Publication Date
Sun Dec 22 2019
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Perceptions and attitudes of community pharmacists towards patient counseling and continuing pharmacy education programs in Iraq
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The pharmacist's role in the community is currently directed towards providing drug information and patient care rather than drug compounding and dispensing. Patient counseling is an essential skill for pharmacists. So as to improve the pharmacist role in the community and enhance the patient's education and counseling skills, many continuing education programs are established. The aim of this study is to assess the perceptions and tendency of community pharmacists in Iraq regarding patients counseling and continuing pharmacists’ educational programs.

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Publication Date
Sun Oct 19 2025
Journal Name
Lecture Notes In Networks And Systems
Utilizing Artificial Intelligence Tools in Enhancing Training of Trainers (ToT) Programs: Modern Approaches and Practical Applications
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This study specifically contributes to the urgent need for novel methods in Training of Trainers (ToT) programs which can be more effective and efficient through incorporation of AI tools. By exploring scenarios in which AI could be used to dramatically advance trainer preparation, knowledge-sharing, and skill-building across sectors, the research aims to understand the possibility. This study uses a mixed-methods approach, it surveys 500 trainers and conducts in-depth interviews with a further 50 ToT program directors across diverse industries to evaluate the impact of AI-enhanced ToT programs. The results showcase that the use of AI has a substantial positive effect on trainer performance and program outcomes. AI-enhanced ToT programs, fo

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Publication Date
Mon Jan 02 2012
Journal Name
Journal Of The Faculty Of Medical Baghdad
Comparative study between ultrasound findings and intra-operative in non-traumatic abdominal pain
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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Comparative Evaluation of Roundabout Capacities Methods for Single-lane and Multi-lane Roundabout
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A roundabout is a highway engineering concept meant to calm traffic, increase safety, reduce stop-and-go travel, reduce accidents and congestion, and decrease traffic delays. It is circular and facilitates one-way traffic flow around a central point. The first part of this study evaluated the principles and methods used to compare the capacity methods of roundabouts with different traffic conditions and geometric configurations. These methods include gap acceptance, empirical, and simulation software methods. Previous studies mentioned in this research used various methods and other new models developed by several researchers. However, this paper's main aim is to compare different roundabout capacity models for acceptabl

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Publication Date
Mon Feb 15 2021
Journal Name
Drug Delivery And Translational Research
Breast intraductal nanoformulations for treating ductal carcinoma in situ II: Dose de-escalation using a slow releasing/slow bioconverting prodrug strategy
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