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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 Jul 27 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Clinicopathological Features of Colorectal Cancer in the Iraqi Population Focusing on Age and Early-Onset of Malignancy: A Descriptive Cross-Sectional Study
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Background: Colorectal cancer (CRC) is one of the top ten most common cancers worldwide. There are multiple risk factors for CRC, one of which is aging. However, in recent years, CRC has been reported in children. Objective: To describe the main characteristics and symptoms of CRC as well as highlight pathologic data for early-onset CRC. Methods: 79 CRC patients were recruited from the Oncology Teaching Hospital in the period February–December 2022. A questionnaire was used to collect demographic and clinical data. Results: 25 (31.6%) of patients were below 50 years of age. 52 (65.8%) patients had tumors in the colon. The most common symptom is bleeding per rectum in both age groups. There was no significant difference in patholog

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Publication Date
Fri Mar 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Relationship Between Competitive Intelligence and Entrepreneurial Performance By Centralizing Strategic Vigilance: Field study of a sample of National colleges in Iraq
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The aim of this study is to highlight the relationship between competitive intelligence and Entrepreneurial Performance by centralizing the strategic vigilance of a sample of civil faculties in Baghdad. The sample of the study was targeted at 10 Iraqi civil colleges, which consisted of (133) members of the faculty council of the faculties, the search data was collected using the questionnaire form as the main research tool. The results showed that the correlation and influence of competitive intelligence and strategic vigilance in the Entrepreneurial Performance, as well as the role of strategic vigilance as an intermediate variable between competitive intelligence and Entrepreneurial Performance.

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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Hydrogen Energy
Optimisation of operating parameters on the performance characteristics of a free piston engine linear generator fuelled by CNG–H2 blends using the response surface methodology (RSM)
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The free piston engine linear generator (FPELG) is a simple engine structure with few components, making it a promising power generation system. However, because the engine works without a crankshaft, the handling of the piston motion control (PMC) is the main challenge influencing the stability and performance of FPELGs. In this article, the optimal operating parameters of FPELG for maximising engine performance and reducing exhaust gas emissions were studied. Moreover, the influence of adding hydrogen (H2) to compressed natural gas (CNG) fuel on FPELG performance was investigated. The influence of operating parameters on in-cylinder pressure was also analysed. The single-piston FPELG fuelled by CNG blended with H2 was used to run the expe

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Publication Date
Sat Jul 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
The Effect of the Combination of Organic Fertilizer and Spraying with Silicon and Calcium on the Growth and Production of Three Cultivars of Beet
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Abstract<p>Field experiments were carried out for the autumn season 2022- 2021 in the field of College of Agricultural Engineering Sciences - University of Baghdad - Jadiriyah Complex –Station A- to study a combination of organic fertilizer (Vermicompost) and cow manure as well as a control treatment (soil only) intertwined with Spraying with silicon, calcium and distilled water (control) in the growth and production of three cultivars of beet (Cylindra, Dark Red, Red) within the design of Completely Randomized Block Design at three replications, The number of treatments was 9 for each replicate. The means were compared according to the least significant difference (L.S.D) at a probability lev</p> ... Show More
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Publication Date
Mon Nov 24 2025
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 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
Fri Jan 01 2016
Journal Name
World Scientific News
Effect of annealing temperature on the structural and optical properties of CdSe: 1% Ag thin films
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Publication Date
Sun Oct 01 2023
Journal Name
Journal Of Taibah University Medical Sciences
Histological evaluation of the effects of bone morphogenetic protein 9 and angiopoietin 1 on bone healing
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Publication Date
Sun Dec 04 2011
Journal Name
Baghdad Science Journal
Use of cefoxitin as indicator for detection of Methicillin Resistant Staphylococcus aureus
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Rapid and accurate identification of Methicillin Resistant Staphylococcus aureus is essential in limiting the spread of this bacterium. The aim of study is the detection of Methicillin Resistant Staphylococcus aureus (MRSA) and determining their susceptibility to some antimicrobial agent. A total of fifty clinical Staphylococcus aureus, isolated from the nose of health work staff in surgery unit of Kalar general hospital and from ear of patients attended to the same hospital. The susceptibilities of isolates were determined by the disc diffusion method with oxacillin (1 ?g) and cefoxitin (30 ?g), and by the mannitol salt agar supplemented with cefoxitin (MSA-CFOX), susceptibilities of isolates to other antimicrobial agent were determined b

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Publication Date
Tue Oct 22 2024
Journal Name
Hemoglobin
Prevalence and Molecular Characterization of β-Thalassemia in Kirkuk Province of Northern Iraq
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