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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 Oct 18 2018
Journal Name
European Journal Of Organic Chemistry
PdII-Mediated Oxidative Amination for Access to a 9-Azabicyclo[4.2.1]nonane Compound Library and Anatoxin-a
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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Effect of the Aquatic Plant Hydrella vorticellata as a Fertilizer on Seed Germination and some Chemical and Cytogenetics Parameters in the cell of Hordeum vulgare and Vicia faba
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The present study is concerned with studying the effect of aquatic plant Hydrella vorticellata with the concentration of 10 and 20 gm/2 K gm soil on percentage and growth rate of germinating seeds of Hordeum vulgare and Vicia faba. More overs, the quantitative amount of NPK in both tested plants and Hydrella vorticellata, are estimated as an organic fertilizer. It has also been find the total number of root cells, the number of dividing cells, and stages of mitosis. The study reveales, that there are no significant differences between the concentration of hydrella used in germination percentage, growth rate, wet and dry weight. While there are differences in the plants containing NPK. The number of cells dividing stages and number of divid

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Publication Date
Mon Jun 16 2025
Journal Name
مجلة كلية التربية الاساسية
A MINI-REVIEW ON THE FABRICATION OF EXPANDED GRAPHITE AND ITS METAL OXIDE COMPOSITES FOR THE PHOTODEGRADATION OF DYES
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This mini review provides an overview of methods for manufacturing expanded graphite (EGT) and the use of its composites with metal oxides in the field of photodegradation of dyes. Dyes from textile manufacturing represent a significant environmental pollution problem in waterways worldwide, highlighting the need for environmentally friendly and efficient technologies to remove dyes from industrial and local wastewater. Photodegradation technologies offer a low-cost, sustainable solution with minimal secondary pollution. Carbon-based materials, such as expanded graphite, are advantageous in enhancing catalytic activity. Accordingly, this review will explore the different fabrication techniques of expanded graphite and summarize the recent d

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
A novel online coupling of ion selective electrode with the flow injection system for the determination of vitamin B1
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A simple, fast, selective of a new flow injection analysis method coupled with potentiometric detection was used to determine vitamin B1 in pharmaceutical formulations via the prepared new selective membranes. Two electrodes were constructed for the determination of vitamin B1 based on the ion-pair vitamin B1-phosphotungestic acid (B1-PTA) in a poly (vinyl chloride) supported with a plasticized di-butyl phthalate (DBPH) and di-butyl phosphate (DBP). Applications of these ion selective electrodes for the determination of vitamin B1 in the pharmaceutical preparations for batch and flow injection systems were described. The ion selective membrane exhibited a near-Nernstian slope values 56.88 and 58.53 mV / decade, with the linear dy

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Publication Date
Tue Apr 01 2025
Journal Name
Georgian Medical News
THE EFFECT OF SOFT ROBOTIC GLOVE ON THE FLEXION AND EXTENSION OF HAND FOR STROKE PATIENTS: A CLINICAL TRIAL
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Background: Stroke defined by diminished cerebral blood flow, results in brain damage and neurological impairments. It often leads to considerable difficulties, such as limited mobility and compromised hand function, usually manifesting as a weakening in the ability to open and shut the hand. Objective: The study evaluates the differences between opening and closing hands when utilizing a soft robot. Methods: The study was conducted in the Mosul Specialist Rehabilitation Center which involved 68 participants, all over 20 years old, with visual impairments. The Iranian Clinical Trials Registry and Ministry of Planning approved the study, The Fugl-Meyer Assessment for Upper Extremity Action Research Arm Test, and Arm Motor Ability Test were

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Publication Date
Thu Mar 21 2024
Journal Name
Egyptian Journal Of Medical Human Genetics
Low heterozygosity for rs3811050, a 5 prime untranslated region variant of the gene encoding interleukin-38 (IL1F10), is associated with a reduced risk of systemic lupus erythematosus
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Abstract<sec> <title>Background

Interleukin-38 (IL-38), an inflammatory cytokine discovered in recent years, has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). IL-38 is encoded by the IL1F10 (interleukin 1 family member 10) gene. Genetic variants of this gene have been associated with susceptibility to a number of autoimmune and inflammatory diseases, while their association with SLE risk has not been explored. In this case–control study, two novel variants of the 5 prime untranslated region (5′UTR) of the IL1F10 gene, rs3811050 C/T and rs3811051 T/G, were investigated

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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
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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