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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
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Calibration and verification of the hydraulic model for Blue Nile river from Roseires dam to Khartoum city
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This research represents a practical attempt applied to calibrate and verify a hydraulic model for the Blue Nile River. The calibration procedures are performed using the observed data for a previous period and comparing them with the calibration results while verification requirements are achieved with the application of the observed data for another future period and comparing them with the verification results. The study objective covered a relationship of the river terrain with the distance between the assumed points of the dam failures along the river length. The computed model values and the observed data should conform to the theoretical analysis and the overall verification performance of the model by comparing it with anothe

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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
Fitting Scoring Rubrics for Electronic Portfolio to Partial Credit Model According to the Number of Assumed Dimensions
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Abstract

 

The current research aims to reveal the extent to which all scoring rubrics data for the electronic work file conform to the partial estimation model according to the number of assumed dimensions. The study sample consisted of (356) female students. The study concluded that the list with the one-dimensional assumption is more appropriate than the multi-dimensional assumption, The current research recommends preparing unified correction rules for the different methods of performance evaluation in the basic courses. It also suggests the importance of conducting studies aimed at examining the appropriateness of different evaluation methods for models of response theory to the

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Publication Date
Wed Jul 09 2025
Journal Name
Resources
Enhancing Reservoir Modeling via the Black Oil Model for Horizontal Wells: South Rumaila Oilfield, Iraq
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Horizontal wells have revolutionized hydrocarbon production by enhancing recovery efficiency and reducing environmental impact. This paper presents an enhanced Black Oil Model simulator, written in Visual Basic, for three-dimensional two-phase (oil and water) flow through porous media. Unlike most existing tools, this simulator is customized for horizontal well modeling and calibrated using extensive historical data from the South Rumaila Oilfield, Iraq. The simulator first achieves a strong match with historical pressure data (1954–2004) using vertical wells, with an average deviation of less than 5% from observed pressures, and is then applied to forecast the performance of hypothetical horizontal wells (2008–2011). The result

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Publication Date
Fri Sep 15 2023
Journal Name
History Of Medicine
The multifaceted role of Dectin-1 and Card9 in inflammatory bowel disease Iraqi patients
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The study aimed to investigate the role of Dectin-1 and Card-9 in pathogenicity of inflammatory bowel disease (IBD). This investigations involved 150 blood samples for IBD patients which divided in to two groups (50 for crohns disease CD (G2) and 50 for ulcerative colitis UC (G3)). All a apparently (male and female) attended to) Al-Kindy hospital) in Baghdad city, department of Gastroenterology. and all of thin were diagnosis by consulters medical staff and pathologists with age range 15-65years average 40 years. in addition to 50 blood samples were collected from apparently healthy individuals as control group (G1). 10 ml were withdrawn from all participants, 5ml for the immunological study which carried by ELISA technique and 5 ml used fo

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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)
The In Situ Expression of IL-6 and IL-1? in breast cancer patients
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Breast cancer is the second most common cancer in women world. Multiple Cytokines appear to have a dominant role in human breast cancer formation. Estimation of the in situ expression of  IL-6 and IL-1β in breast cancer patients. A sixty patients with breast cancer BC were divided into two clinical subgroups, (30) with malignant breast cancer MBC and (30) with benign breast tumor as a control group according to histological examination. In situ hybridization technique used for detection of IL-6 and IL-1β mRNA sequence in two groups.  The results showed that percentages of mRNA expression of IL-6 and IL-1β were in (≥ 11-50%) for malignant breast cancer. This research also investigated that (73.3%) of beni

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Publication Date
Fri Dec 22 2017
Journal Name
Pakistan Journal Of Biotechnology
THE ROLE OF HLA-DRB 1 ALLELE IN HYPOTHYROID PATIENTS WITH AND WITHOUT PERIODONTITIS
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Hypothyroidism is a frequent disorder in the general population, especially among women, is defined as adeficiency of thyroid activity that results from insufficient production or action of thyroid hormones leading to a totaldecrease of metabolic. Human leukocyte antigen is the most polymorphic genetic system in man. Genes of this regioninfluence susceptibility to certain diseases.Objectives: The purpose of the present study is to investigate the role of HLA-DRB1 genotyping in hypothyroidpatients with and without periodontitis. Sixty hypothyroid patients 30 of patients were with periodontitis and 30without periodontitis compare with 30 healthy subjects as control enrolled in this study. DNA was extracted fromblood samples, then HLA- genotyp

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Publication Date
Wed Aug 30 2023
Journal Name
Baghdad Science Journal
Comparative Analysis of MFO, GWO and GSO for Classification of Covid-19 Chest X-Ray Images
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Medical images play a crucial role in the classification of various diseases and conditions. One of the imaging modalities is X-rays which provide valuable visual information that helps in the identification and characterization of various medical conditions. Chest radiograph (CXR) images have long been used to examine and monitor numerous lung disorders, such as tuberculosis, pneumonia, atelectasis, and hernia. COVID-19 detection can be accomplished using CXR images as well. COVID-19, a virus that causes infections in the lungs and the airways of the upper respiratory tract, was first discovered in 2019 in Wuhan Province, China, and has since been thought to cause substantial airway damage, badly impacting the lungs of affected persons.

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Publication Date
Thu Jan 23 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
EFFECT OF DECISION OF INCREASING THE MINIMUM LIMIT OF THE CAPITAL IN THE IRAQI PRIVATE BANKING ACTIVITY: APPLIED STUDY IN A SAMPLE OF PRIVATE IRAQI BANKS
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This research aims to show the sight at the importance of the private banking sector in Iraq and its role in financing of the investment projects , of the ability of Central Bank's decision to increase the minimum limit of capital for private banks to provide support to the economic activity and the development in Iraq. In addition to illustrate the importance of the capital increase, with a, and taking into notice the most important determinants that can stand in front of these banks in the beginning of the decision implementation, which in turn can lead to the most important proceedings that can contribute in the support of banks to implementation the decision.  Also, the research has highlighted the most important ways through wh

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Publication Date
Mon Oct 20 2025
Journal Name
Научный форум
Strategies of cultural adaptation and linguistic russification in the muravyov-kistyakovsky translation of 'the fellowship of the ring' (1982): a comprehensive study of fantasy text domestication
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This study examines strategies of cultural domestication in Muravyov and Kistyakovsky’s Russian translation of (The Fellowship of the Ring). It documents transformations of character names, toponyms, dialogues, and cultural references, highlighting systematic Russification and the infusion of Soviet political commentary that reshape the text into cultural rewriting.

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Visibal management and its implications for Organizational culture A survey of a sample of R & D staff / Ministry of Higher Education and Scientific Research
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The research aims to shed light on the concept of Visibal management and its reflection on the organizational culture of the organization. The visual administration is a modern administrative method that contributes to the renewal and development of the organization's reality through surveying the opinions of a sample of 61 employees in the R & D / Ministry of Higher Education and Scientific Research. (130) individuals. The questionnaire was used as a main tool for collecting data and information, and their answers were analyzed using the SPSS program in data entry and analysis. The most important tools are computational circles, standard deviations, method of analysis and regression equation. There is a possibility to apply

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