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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 Jan 01 2025
Journal Name
Aip Conference Proceedings
Enhanced aerodynamics for sport cars using inverted wings: A comprehensive review
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Publication Date
Tue Jan 01 2008
Journal Name
Journal Of Engineering
USING FUZZY LOGIC CONTROLLER FOR A TWO- TANK LEVEL CONTROL SYSTEM
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This paper presents a fuzzy logic controller for a two-tank level control system, which is a process with a dead time. The fuzzy controller is a proportional-integral (PI-like) fuzzy controller which is suitable for steady state behavior of the system. Transient behavior of the system was improved without the need for a derivative action by suitable change in the rule base of the controller. Simulation results showed the step response of the two-tank level control system when this controller was used to control this plant and the effect of the dead time on the response of the system.

Publication Date
Sun Jun 02 2019
Journal Name
Baghdad Science Journal
Proposing a Scheme for Human Interactive Proof Test using Plasma Effect
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            Human Interactive Proofs (HIPs) are automatic inverse Turing tests, which are intended to differentiate between people and malicious computer programs. The mission of making good HIP system is a challenging issue, since the resultant HIP must be secure against attacks and in the same time it must be practical for humans. Text-based HIPs is one of the most popular HIPs types. It exploits the capability of humans to recite text images more than Optical Character Recognition (OCR), but the current text-based HIPs are not well-matched with rapid development of computer vision techniques, since they are either vey simply passed or very hard to resolve, thus this motivate that

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Publication Date
Mon Jan 01 2024
Journal Name
Medical Research Archives
Genetic Polymorphism for the Gene Encoding Endoplasmic Reticulum Aminopeptidase-1 (ERAP-1) in Iraqi Patients with Ankylosing Spondylitis
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Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. This study was aimed to investigate the relationship between the rs27044 polymorphism in Endoplasmic reticulum aminopeptidase-1 (ERAP-1) with the susceptibility and severity of AS correlated with some biochemical markers such as hematological parameter (Erythrocytes sedimentation rate (ESR)) and immunological parameters (C-reactive protein (CRP), Human leukocyte antigen-B27 (HLA-B27), Interlukin-6 (IL-6) and Interlukin-23 (IL-23)), and oxidative stress parameters (Glutathione (GSH) and Malondialdehyde (MDA)) in a sample of Iraqi population. A total of 60 blood samples were collected from AS patients requited Rhe

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Publication Date
Tue Jul 01 2014
Journal Name
International Journal Of Artificial Intelligence And Mechatronics
Machining Polylines and Ellipses using Three-Axis CNC Milling Machine
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CNC machine is used to machine complex or simple shapes at higher speed with maximum accuracy and minimum error. In this paper a previously designed CNC control system is used to machine ellipses and polylines. The sample needs to be machined is drawn by using one of the drawing software like AUTOCAD® or 3D MAX and is saved in a well-known file format (DXF) then that file is fed to the CNC machine controller by the CNC operator then that part will be machined by the CNC machine. The CNC controller using developed algorithms that reads the DXF file feeds to the machine, extracts the shapes from the file and generates commands to move the CNC machine axes so that these shapes can be machined.

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Publication Date
Sun Jan 30 2022
Journal Name
Gsc Biological And Pharmaceutical Sciences
Comparative anatomical study for fruits of some species of Bunium L. (Umbelliferae) in Iraq
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Bunium is one of the interested genus that grow in different region of Iraq, it is within the family Umbelliferae (Apiaceae), and the species within this family have a considerable fruit characteristics. The species that were chosen in this study are: B. brachyactis (Post) H. Wolff, B. caroides (Boiss.) Hausskn. Ex Bornm., B. chaerophylloides (Regel& Schmalh.) Drude, B. rectangulum Boiss. & Hausskn., B. verruculosum C.C.Towns. and B. avromanum (Boiss.& Hausskn) Drude., the study found that the fruits of these species have 5 protrusions different in size but all have the same number of vittae, but some are semiler in size and some are not, the number of vascular element are varied between these species, anatomical charact

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Publication Date
Sun Oct 12 2025
Journal Name
Al–bahith Al–a'alami
Graduate Media Students’ Satisfaction Level in Their Program of Study:  The level of Satisfaction about the Study Programs of the masters of Media students / Case Study of Media faculties’ students at “Yarmouk University,
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The current study is considered a field study to measure the level of satisfaction of the academic programs of Media Masters students. That was accomplished through surveying the attitudes of the students who are enrolled in the faculties of media at the following universities: (Petra University, The Middle East University (MEU), and Al-Yarmouk University). Those students were enrolled in the master’s program within the formal educational system during the second semester of the academic year (2015 – 2016). This survey aims to identify the services, facilities and academic programs provided by the concerned faculties. It, also, aims to identify the public relations, administrative, educational and services aspects of those faculties.

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Publication Date
Tue Dec 07 2021
Design and numerical verification of a polarization-independent grating coupler using a double-layer approach for visible wavelengths applications
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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Intelligent Systems
Trip generation modeling for a selected sector in Baghdad city using the artificial neural network
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Abstract<p>This study is planned with the aim of constructing models that can be used to forecast trip production in the Al-Karada region in Baghdad city incorporating the socioeconomic features, through the use of various statistical approaches to the modeling of trip generation, such as artificial neural network (ANN) and multiple linear regression (MLR). The research region was split into 11 zones to accomplish the study aim. Forms were issued based on the needed sample size of 1,170. Only 1,050 forms with responses were received, giving a response rate of 89.74% for the research region. The collected data were processed using the ANN technique in MATLAB v20. The same database was utilized to</p> ... Show More
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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of International Oral Health
Endothelin-1 is a surrogate biomarker link severe periodontitis and endothelial dysfunction in hypertensive patients: The potential nexus
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Aim and Objectives: The objective of this study was to illustrate the link between periodontitis (PO) and endothelial dysfunction in hypertensive patients. Materials and Methods: This cross‑sectional study involved 53 hypertensive patients with or without PO compared with 28 healthy controls. On the basis of the study protocol, the participants were divided into three groups: Group (1): 24 patients with hypertension only, Group (2): 29 patients with hypertension and PO, and Group (3): 28 healthy controls. Lipid profile, endothelin‑1 (ET‑1), and high‑sensitivity C‑reactive protein (hs‑CRP) were measured. Blood pressure and body mass index (BMI) were evaluated. Diagnostic criteria of severe PO periodontal indices including plaque

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