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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 Jan 21 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Environmental parameters drive the phytoplankton community structure: a case study in Baghdad Tourist Island Lake, Iraq
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Phytoplankton community is a model for of monitoring  aquatic systems and interpreting the environmental change in aquatic systems. The present study aimed to forecast environmental parameters that drive the change of phytoplankton community structure in the lake. The present study was carried out in Baghdad Tourist Island Lake (BTIL) for the period From October 2021 to May 2022. The study included the quality and quantity of phytoplankton, moreover, the highest and lowest value of the physical and chemical parameters were (Water temperature (13-30 °C), Light penetration (94-275cm), electric conductivity (837-1128 µS/cm), salinity (0.5-0.7 ‰), pH (7-8.2), total alkalinity (126-226 mg CaCO3/L), total Hardness (297-395 mg CaCO3/L

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Publication Date
Tue Apr 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Organizational Culture Impact in Enhancing Job Performance A Case Study in the Modern Paint Industries Company
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          The organizational culture is considered as an important topic. In this research, this topic was studied in modern paints Industries Company to assess its role in job performance and to show if there is this relationship between them or no. it is, also, attempted to measure this strength of this relationship if any. The 40 cases research sample was chosen. This sample included the chief executive, his assistants, key managers, and their assistants. The questioner consists of two sets of questions : the first set ( concerning the organizational culture) covers six variables (Physical structures , Symbols

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The impact of enabling the effectiveness of the work of the audit committees in private commercial banks (A survey study of the views of a sample of the objective of the inspection bodies represented by the Central Bank and the Securities Commission and e
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The aim of this study is to identify the effect of enabling the effectiveness of the work of the audit committees in private commercial banks and to identify the extent of awareness of the importance of empowerment in the work of these committees, especially as it is known that these committees, especially the inspection committees that go to private banks and from various sources including committees of the Central Bank of Iraq Committees of the Securities Commission and finally committees of the external audit offices, through an analysis of the determinants of empowerment in the performance of the most important work of the audit committees, namely: supervising the process of preparing reports, supervising the system of intern

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Publication Date
Sun Dec 03 2017
Journal Name
Baghdad Science Journal
A Study of Zooplankton Community in Dukan Lake, Kurdistan Region-Iraq, with a New Record of Craspedacusta sowerbii Lankester (1880) Medusa (Cnidaria: Hydrozoa)
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A study of Zooplankton community has been carried out at four selected sites on Dukan Lake. Samples of water and zooplankton were collected monthly for the period from July 2015 to February 2016. Some physical and chemical properties of water were studied and the results showed that the air temperature were ranged from 0 to 36.16 °C, water temperature ranged from 2.83 to 34.66 °C, hydrogen ion concentration of studied sites were found to lie in alkaline side, it was ranged between 6.87 to 8.57, electrical conductivity ranged from 190.79 to 850.08 µs.cm­¹, turbidity ranged from 0.9-7.7 NTU, and dissolved oxygen from 3.3 to 6.8 mg.l-¹ while BOD5 were ranged from 0.53 to 34.66 mg.l-¹. Concerning to the zooplankton, 37 species were ident

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Publication Date
Thu Dec 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of serum levels of monocyte chemoattractant protein 1 (MCP 1) in patients with periodontitis and atherosclerotic cardiovascular disease
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Background: Monocyte chemotactic protein-1 (MCP-1) is a chemokine expressed by inflammatory and endothelial cells. It has a crucial role in initiating, regulating, and mobilizing monocytes to active sites of periodontal inflammation. Its expression is also elevated in response to pro-inflammatory stimuli and tissue injury, both of which are linked to atherosclerotic lesions. Aim of the study: To determine the serum level of MCP-1 in patients with periodontitis and atherosclerotic cardiovascular disease in comparison to healthy control and evaluate the biomarker's correlations with periodontal parameters. methods: This study enrolled 88 subjects, both males and females, ranging in age from 36-66 years old, and divided into four groups: 1<

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Publication Date
Tue Feb 17 2026
Journal Name
Journal Of Physical Education
Analytical – Comparative Study of Some Kinematical Variables Of Jump Shot and Shooting in Youth Basketball Players
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Publication Date
Tue Feb 17 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of MMP9, as a marker of local invasion in Hodgkin’s and Non-Hodgkin’s lymphoma of the head and neck region
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Background: Malignant lymphoma is the generic term given to tumors of the lymphoid system and specifically of lymphocytes and their precursor cells, While all lymphomas are malignant neoplasms, there is a wide spectrum of clinical behavior, with some following an indolent clinical course and others behaving in an aggressive manner (will causing death in a short time frame if left untreated). The metastatic process involves intravasation and extravasation of tumor cells, followed by reimplantation of tumor cells, formation of a new tumor stoma, Degradation of the extracellular matrix and components of the basement membrane by proteases facilitates the detachment of tumor cells, their crossing of tissue boundaries, and invasion into adjacent

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Publication Date
Wed Jan 01 2020
Journal Name
Research Journal Of Pharmacy And Technology
The effectiveness of topical vitamin k cream 1% in the treatment of steroid-induced rosacea
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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the "Senge" Model of Organizational Learning in the adoption of Total Quality Management principles) Exploratory study in an organization)
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      This study is concerned with organizational learning and its impact on total quality management in the education sector. Organizational learning is a process that provides the educational sector with the ability to adapt and respond rapidly to developments and changes in a better way according to its main dimensions (Mental Models, Personal Mastery, Team Learning, Shared Vision, System Thinking) by adopting the philosophy of Total Quality Management (TQM) in accordance with its basic dimensions (leadership, customer satisfaction, participation of workers, continuous improvement, training and education). The main purpose of this study is to know (the impact of the Senge model of organizational learni

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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the "Senge" Model of Organizational Learning in the adoption of Total Quality Management principles) Exploratory study in an organization)
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      This study is concerned with organizational learning and its impact on total quality management in the education sector. Organizational learning is a process that provides the educational sector with the ability to adapt and respond rapidly to developments and changes in a better way according to its main dimensions (Mental Models, Personal Mastery, Team Learning, Shared Vision, System Thinking) by adopting the philosophy of Total Quality Management (TQM) in accordance with its basic dimensions (leadership, customer satisfaction, participation of workers, continuous improvement, training and education). The main purpose of this study is to know (the impact of the Senge model of organizational learni

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