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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 Jun 20 2024
Journal Name
Acta Facultatis Medicae Naissensis
Clinical properties and seminal fluid analysis of patients with primary infertility consulting the urology outpatient clinic for the first time: A cross-sectional study
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Introduction/Aim. Seminal fluid analysis (SFA) plays a crucial role in helping infertility clinics diagnose the underlying reason of male infertility. The aim of the study was to investigate seminal fluid patterns of male partners of an infertile couple with apparently fertile female partners. Materials and methods. A cross-sectional study was conducted between January 2019 and December 2022. Patients were attending consultations for delayed conception for more than 12 months with apparently fertile female partner. Results. Four hundred fifty-three patients were included in the study. The distribution of patients according to age groups showed that 277 patients were young, aged 21 - 30 years (61%). Two hundred sixty-two (58%) patien

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Publication Date
Thu Oct 31 2019
Journal Name
Al-kindy College Medical Journal
Contraception as a Risk Factor of Trichomonas vaginalis Infection Among Women Attending Outpatient of Al-Batool Teaching Hospital for Maternity and Children-Baqubah-Iraq
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Background:The effects of contraception on Trichomonas vaginalis have important implications for women who suffer from infections associated with disruptions in the vaginal ecology, such as bacterial vaginitis and urinary tract infections.

Objective: To find the association of the common types of contraceptions with the Trichomonasvaginalis infection in women admitted to the Al-BatoolTeaching Hospital for Maternity and Children in Baqubah city.

Type of study: Cross-sectional study

Methods: This study consist of 75 women with contraception use and71 apparently healthy non contraception user women  admitted to outpatient in Al

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Publication Date
Wed Jul 06 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Image Compression using Polynomial Coding Techniques: A review
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Improving IoT Applications Using a Proposed Routing Protocol
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The main objective of this work is to propose a new routing protocol for wireless sensor network employed to serve IoT systems. The routing protocol has to adapt with different requirements in order to enhance the performance of IoT applications. The link quality, node depth and energy are used as metrics to make routing decisions. Comparison with other protocols is essential to show the improvements achieved by this work, thus protocols designed to serve the same purpose such as AODV, REL and LABILE are chosen to compare the proposed routing protocol with. To add integrative and holistic, some of important features are added and tested such as actuating and mobility. These features are greatly required by some of IoT applications and im

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Publication Date
Fri Jan 01 2016
Journal Name
Middle-east Journal Of Scientific Research
Question Classification Using Different Approach: A Whole Review
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Publication Date
Fri Jan 01 2016
Journal Name
Bio-inspired Computing – Theories And Applications
Image Segmentation Using Membrane Computing: A Literature Survey
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Publication Date
Sun Dec 01 2024
Journal Name
Al-khwarizmi Engineering Journal
Defect Detection Using Thermography Camera Techniques: A review
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Individuals across different industries, including but not limited to agriculture, drones, pharmaceuticals and manufacturing, are increasingly using thermal cameras to achieve various safety and security goals. This widespread adoption is made possible by advancements in thermal imaging sensor technology. The current literature provides an in-depth exploration of thermography camera applications for detecting faults in sectors such as fire protection, manufacturing, aerospace, automotive, non-destructive testing and structural material industries. The current discussion builds on previous studies, emphasising the effectiveness of thermography cameras in distinguishing undetectable defects by the human eye. Various methods for defect

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Publication Date
Thu Sep 08 2022
Journal Name
Al-khwarizmi Engineering Journal
Assessment of Ornamental Plants Tolerance for Acute Exposure of Acetaminophen and Methylparaben in Constructed Wetlands- a Preliminary Study
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The study aims to select suitable ornamental plant species that can survive relatively with high concentrations of acetaminophen and methylparaben in constructed wetlands. Alternanthera spp, Asparagus aethiopicus and Chlorophytum comosum are examined to withstand three initial concentrations, 20, 100 and 200 mg/L of acetaminophen and methylparaben. A total of 21 plastic pails with each 3 L capacity consisting of nine pails are used for each pharmaceutical and personal care products (PPCPs) compounds (acetaminophen and methylparaben) for three ornamental plants (Alternanthera spp, Asparagus aethiopicus and Chlorophytum comosum), with three pails as plant controls. The results reveales

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Publication Date
Fri Mar 28 2025
Journal Name
Journal Of Physical Education
Special exercises using tools and their effect on teaching the skill of a front shoulder circle on the rings apparatus in artistic gymnastics for students
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Sports skills in some individual games require physical and motor qualities to facilitate the process of skill performance and also require the instructor or trainer to use more than one strategy, method and way to bring the performance to the level of mastery and avoid injury. The aim of the research is to know the effect of using special exercises using tools and their effect on teaching the skill of a front shoulder circle. The research hypothesis is that using special exercises with tools has a positive effect on teaching the skill of a front shoulder circle on the rings apparatus. Research method: - The researchers used the experimental method by designing two equal groups, the control and the experimental, to suit the research

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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
Fuzzy-assignment Model by Using Linguistic Variables
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      This work addressed the assignment problem (AP) based on fuzzy costs, where the objective, in this study, is to minimize the cost. A triangular, or trapezoidal, fuzzy numbers were assigned for each fuzzy cost. In addition, the assignment models were applied on linguistic variables which were initially converted to quantitative fuzzy data by using the Yager’sorankingi method. The paper results have showed that the quantitative date have a considerable effect when considered in fuzzy-mathematic models.

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