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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 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Calibrating the Reservoir Model of the Garraf Oil Field
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   History matching is a significant stage in reservoir modeling for evaluating past reservoir performance and predicting future behavior. This paper is primarily focused on the calibration of the dynamic reservoir model for the Meshrif formation, which is the main reservoir in the Garraf oilfield. A full-field reservoir model with 110 producing wells is constructed using a comprehensive dataset that includes geological, pressure-volume-temperature (PVT), and rock property information. The resulting 3D geologic model provides detailed information on water saturation, permeability, porosity, and net thickness to gross thickness for each grid cell, and forms the basis for constructing the dynamic reservoir model. The dynamic reservoir mo

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The impact of managing employees' performance in building intellectual capital Analytical study of the views of a sample of heads of scientific departments At the University of Kirkuk
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The research aims to identify the impact of managing performance's employees in building intellectual capital, Because employing the practice of managing the performance of employees may acquire familiar skills to improve their performance and reflect on the construction of intellectual capital in the surveyed area, Especially that the independent dimension represented by the management of the performance of employees is one of the important topics that has received attention in the world of management in general and human resource management in particular.  While the adopted dimension was represented by Intellectual capital in the important practice of human resource management in the increasing of  their knowledge, to

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Publication Date
Thu Mar 05 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status and salivary enzymes level in smokers and non-smokers (comparative, cross sectional study)
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Background: Smoking is considering a major risk factor for development and progression of periodontal disease. Investigations regarding the association between smoking and periodontal disease have consistently demonstrated negative periodontal effects and greater probabilities of established periodontal disease among smokers in comparison with non smokers. The purpose of this study was to evaluate the effects of smoking on periodontal health status and on the salivary levels of alkaline phosphatase (ALP), lactate dehydrogenase (LDH) and creatine kinase (CK), and to correlate the clinical parameters of periodontal health with the biochemical findings in smokers and non-smokers. Materials and methods: Unstimulated saliva sample was collected

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Publication Date
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
Comparative Study between RIPASA Scoring System and ALVARADO Scoring System in Diagnosing Acute Appendicitis in Adults
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Background: Acute appendicitis is regarded as one of the most common inflammation that needs surgical intervention. Different scoring systems have been used for diagnosing of acute appendicitis. ALVARADO score is one of the most widely used score in diagnosing of acute appendicitis, but the accuracy of the latter is insufficiently low in Middle-East patients. Thus a new scoring system called RIPASA score has been designed for diagnosing of acute appendicitis in those patients. The aim of this study is to use RIPASA score and compare its result with ALVARADO score in diagnosing of acute appendicitis.

Subjects and Methods: The study includes 200 patients with symptoms and signs of

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Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Creative thinking and its impact on reengineering hotel service )Comparative field study in premium class hotels(
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The research seeks to identify the dimensions of creative thinking and its impact on the re-engineering of hotel service operations by analyzing the correlation and impact between research variables as well as comparing the research sample The importance of the research comes from the need to motivate managers the importance of creative thinking among workers in the researched hotels because it is an essential part in the re-engineering of hotel services. To achieve this a questionnaire was designed containing (33) items that include the independent research variables (creative thinking) and the accredited (re-engineering the hotel service) and distributed to a sample of (50) individuals represented by (Commissioner Director, Dep

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Publication Date
Thu Mar 05 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the effect of Autolougues Platelet Rich Fibrin Matrix on osseointegration of the titanium implant immunohistochemical evaluation for PDGF-I&IGF-A
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Background: Platelet-rich fibrin (PRF) is a simple, low cost and minimally invasive way to obtain a natural concentration of autologous growth factors and is currently being widely experimented in different fields of medicine for its ability to aid the regeneration of tissue with a low healing potential. Fields of application are sports medicine, orthopedics, dentistry, dermatology, ophthalmology, plastic and maxillofacial surgery, etc. The rationale for using platelets in so many fields for the treatment of different tissues is because PLTs constitute a reservoir of critical GFs and cytokines, which may govern and regulate the tissue healing process that is quite similar in all kinds of tissues. Materials and Methods: Screw titanium implan

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Publication Date
Wed Jan 01 2025
Journal Name
Smart Innovation, Systems And Technologies
The Effect of Two Training Approaches with (Hanging–Heavy) Ropes in Developing Some Physical Abilities and Accuracy of Shooting—In Front of Handball
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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Use ofBang marking in the management of the cost of food and beverages in the hotel: sector (Case study in a sample of hotels in Baghdad governorate)
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The competition in the hotel sector, globalization and the development of new information have forced the sector to continuously seek new techniques and arrangements to remain competitive through hotel industry companies, including Benchmarking and the application of this method in the hotel sector. The selection of the Rashid International Hotel by the Ministry of Tourism as a leading hotel or benchmark for comparison of other hotels in Iraq, and the selection of two hotels in Baghdad for comparison, namely (Ishtar International Hotel, Baghdad International Hotel) and the choice also by the Ministry of Tourism, N is to correct the course of practice to manage the cost and diagnosis of the weakness of the strengths and weaknesses in the

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Publication Date
Thu Mar 05 2026
Journal Name
Iraqi Journal For Administrative Sciences
Using the Statistical Analysis to study the important reasons of the pollution in the Iraqi Marshlands Areas
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The need for detection and investigation of the causes of pollution of the marshes and submit a statistical study evaluated accurately and submitted to the competent authorities and to achieve this goal was used to analyze the factorial analysis and then obtained the results from this analysis from a sample selected from marsh water pollutants which they were: (Electrical Conductivity: EC, Power of Hydrogen: PH, Temperature: T, Turbidity: TU, Total Dissolved Solids: TDS, Dissolved Oxygen: DO). The size of sample (44) sites has been withdrawn and examined in the laboratories of the Iraqi Ministry of Environment. By illustrating SPSS program) the results had been obtained. The most important recommendation was to increase the pumping of addit

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Publication Date
Wed Mar 23 2022
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a strategy (fahs) in the development of grammar skills of a sample of secondary school Female Students in Saudi Arabia
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The aim of the present research is to measure the degree of strategic effectiveness (fahs) in the development of grammar skills of high school students in the Kingdom of Saudi Arabia and to achieve the goal of the researcher the researcher used the semi-experimental approach; On ten arbitrators specializing in grammar, morphology, curricula and methods of teaching the Arabic language. After confirming the validity of the guideline, the researcher prepared an achievement test consisting of (22) paragraphs of the type of short answer and multiple choice. The researcher trained a teacher to apply the strategy to the experimental research sample using the (screening) component of (30) students, and the same parameter taught the control sampl

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