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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
Wed Nov 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Genders identification using mandibular canines(Iraqi study)
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Background: This study aimed to determine the gender of a sample of Iraqi adults using the mesio-distal width of mandibular canines, inter-canine width and standard mandibular canine index, and to determine the percentage of dimorphism as an aid in forensic dentistry. Materials and methods: The sample included 200 sets of study models belong to 200 subjects (100 males and 100 females) with an age ranged between 17-23 years. The mesio-distal crown dimension was measured manually, from the contact points for the mandibular canines (both sides), in addition to the inter-canine width using digital vernier. Descriptive statistics were obtained for the measurements for both genders; paired sample t-test was used to evaluate the side difference of

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Publication Date
Fri Apr 15 2016
Journal Name
Research Journal Of Applied Sciences, Engineering And Technology
Development of Measurement Scale for Hypothesized Conceptual Model of E-service Quality and User Satisfaction Relationship
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Publication Date
Wed Jun 01 2022
Journal Name
International Journal Of Early Childhood Special Education
A study of the level of skill self-esteem and some aspects of attention (acute - focus - diversion) and their relationship to the performance of the spiking and serve among young tennis players
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The purpose of this paper is to identifying the level of skill self-esteem of the young tennis players in the Governorate of Baghdad, identifying some aspects of attention (acuteness, concentration, and diversion of attention) among the young tennis players of the Baghdad governorate, and identify the skills of serve and serve spiking in tennis by young tennis players in Baghdad governorate. The researchers used the descriptive approach in the correlative relations style for its suitability and the research problem. the research sample was chosen in a deliberate way from the youth team players in tennis for the Governorate of Baghdad and the participants in the 2021-2022 sports season, whose number is (20) male players and (4) young playe

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Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The role of organizational change in easing the organizational conflict: an exploratory study of the opinions of a sample of managers and workers in Iraq to EarthLink Network Services Company And communications
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Research on the role of organizational change in easing the organizational conflict focuses for being one of the important topics and relatively modern and which have a significant impact on the future of organizations, so this study was to identify the relationship and the impact of organizational change and of deportation (technological, organizational structure, human resources, the change in the task) at the organizational conflict in the Earth company link Iraq, in order to reach the goals of the research, it has been the development of a questionnaire distributed to a random sample of (100) composed employees from managers and heads of departments and the people and staff at the Earth company link Iraq, the study found: the

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Publication Date
Wed Apr 01 2020
Journal Name
2020 International Conference On Computer Science And Software Engineering (csase)
Implementing a Super Decisions Software (SDS) in a Transport Sector
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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Risk-Based Inspection Due to Corrosion Consequences for Oil and Gas Flowline: A Review
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   The petroleum industry, which is one of the pillars of the national economy, has the potential to generate vast wealth and employment possibilities. The transportation of petroleum products is complicated and changeable because of the hazards caused by the corrosion consequences. Hazardous chemical leaks caused by natural disasters may harm the environment, resulting in significant economic losses. It significantly threatens the aim for sustainable development. When a result, determining the likelihood of leakage and the potential for environmental harm, it becomes a top priority for decision-makers as they develop maintenance plans. This study aims to provide an in-depth understanding of the risks associated with oil and gas pipeli

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Publication Date
Wed Jan 25 2023
Journal Name
Molecular Simulation
Engineering promising A-π-D type molecules for efficient organic-based material solar cells
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Within this work, to promote the efficiency of organic-based solar cells, a series of novel A-π-D type small molecules were scrutinised. The acceptors which we designed had a moiety of N, N-dimethylaniline as the donor and catechol moiety as the acceptor linked through various conjugated π-linkers. We performed DFT (B3LYP) as well as TD-DFT (CAM-B3LYP) computations using 6-31G (d,p) for scrutinising the impact of various π-linkers upon optoelectronic characteristics, stability, and rate of charge transport. In comparison with the reference molecule, various π-linkers led to a smaller HOMO–LUMO energy gap. Compared to the reference molecule, there was a considerable red shift in the molecules under study (A1–A4). Therefore, based on

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
A New Fractal Printed Dipole Antenna Based on Tent Transformations for Wireless Communication Applications
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In this paper, a compact multiband printed dipole antenna is presented as a candidate for use in wireless communication applications. The proposed fractal antenna design is based on the second level tent transformation. The space-filling property of this fractal geometry permits producing longer lengths in a more compact size. Theoretical performance of this antenna has been calculated using the commercially available software IE3D from Zeland Software Inc. This electromagnetic simulator is based on the method of moments (MoM). The proposed dipole antenna has been found to possess a considerable size reduction compared with the conventional printed or wire dipole antenna designed at the same design frequency and using the same substrate

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
ZnO: MWCNT optical hybrid filter a promising nanomaterial for wastewater treatment and antimicrobial applications
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Publication Date
Wed Mar 10 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A hybrid Grey Wolf optimizer with multi-population differential evolution for global optimization problems
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