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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
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
The Role of Local Satellite Channels in the formation of knowledge and trends of the Iraqi Public Towards Terrorism: A Field Study
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Terrorism is a global phenomenon that engulfs most regions of the world to varying degrees. Media outlets are aware of the many incidents of violence and terrorism that have increased in recent times. The differences between the size of the phenomenon in different societies are the causes and severity of the phenomenon. On the role of local satellite channels in shaping the knowledge and trends of the Iraqi public towards the events of terrorism, in light of the assumptions of reliance on the media. The importance of this study is that it assesses the role of local satellite channels in the formation of knowledge and trends The study seeks to know the extent of exposure of the Iraqi public to local satellite channels, and to reveal the e

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Chaotic behaviour of the Rossler model and its analysis by using bifurcations of limit cycles and chaotic attractors
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The behaviour of certain dynamical nonlinear systems are described in term as chaos, i.e., systems' variables change with the time, displaying very sensitivity to initial conditions of chaotic dynamics. In this paper, we study archetype systems of ordinary differential equations in two-dimensional phase spaces of the Rössler model. A system displays continuous time chaos and is explained by three coupled nonlinear differential equations. We study its characteristics and determine the control parameters that lead to different behavior of the system output, periodic, quasi-periodic and chaos. The time series, attractor, Fast Fourier Transformation and bifurcation diagram for different values have been described.

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Publication Date
Sun Nov 23 2025
Journal Name
Journalnx
Review Article: Impact of Molecular Biology in Life Science
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To study and understand the mechanism of living systems, and how it works, it is quite important to investigate it at molecular level (like genomic, proteomic) as well as the methodologies, and how to apply and imply it on different branch of sciences and how can use it in developing medical diagnosis, treatments, drugs, and increased it in the future. Additionally it can also be applied in forensic techniques, food production and agriculture, as well as genetic profiling. This can be well understand by interfering and combinations of all branches of life sciences such as chemistry, physics, biotechnology, genetic evolution, and minimize the gap between them, this

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Publication Date
Wed Jun 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Molecular Detection of Porphyromonas gingivalis in COVID-19 Patients
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Background:SARS-CoV-2 infection has caused a global pandemic that continues to negatively impact human health. A large group of microbial domains including bacteria co-evolved and interacted in complex molecular pathogenesis along with SARS-CoV-2. Evidence suggests that periodontal disease bacteria are involved in COVID-19, and are associated with chronic inflammatory systemic diseases. This study was performed to investigate the association between bacterial loads of Porphyromonas gingivalis and pathogenesis of SARS-CoV-2 infection. Fifty patients with confirmed COVID-19 by reverse transcriptase-polymerase chain reaction, their age ranges between 20-76 years, and 35 healthy volunteers (matched accordingly with age and sex to th

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Publication Date
Fri Jun 17 2022
Journal Name
International Journal Of Health Sciences
Molecular detection of biofilm coding genes in Staphylococcus aureus
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In accordance with epidemic COVID-19, the elevated infection rates, disinfectant overuse and antibiotic misuse what led to immune suppression in most of the population in addition to genotypic and phenotypic alterations in the microorganisms, so a great need to reevaluate the genetic determinants that responsible for bacterial community (biofilm) has been raised. A total of 250 clinical specimens were obtained from patients in Baghdad hospitals and streaked on Mannitol salt agar medium. The results revealed that 156 isolates appeared as round yellow colonies, indicating that they were mostly identified as Staphylococcus aureus from 250 specimens. The antibiotic resistance pattern of the isolates for methicillin 37.17% (n=58), Amoxic

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Publication Date
Mon Mar 09 2015
Journal Name
Monthly Notices Of The Royal Astronomical Society
A reliable iterative method for solving Volterra integro-differential equations and some applications for the Lane–Emden equations of the first kind
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Publication Date
Tue Dec 07 2021
Journal Name
Tencon 2021 - 2021 Ieee Region 10 Conference (tencon)
Robust State Feedback Control of Electric Heating Furnace Using a New Disturbance Observer
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As one type of heating furnaces, the electric heating furnace (EHF) typically suffers from time delay, non-linearity, time-varying parameters, system uncertainties, and harsh en-vironment of the furnace, which significantly deteriorate the temperature control process of the EHF system. In order to achieve accurate and robust temperature tracking performance, an integration of robust state feedback control (RSFC) and a novel sliding mode-based disturbance observer (SMDO) is proposed in this paper, where modeling errors and external disturbances are lumped as a lumped disturbance. To describe the characteristics of the EHF, by using convection laws, an integrated dynamic model is established and identified as an uncertain nonlinear second ord

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Publication Date
Thu Mar 12 2020
Journal Name
Al-khwarizmi Engineering Journal
Inverse Kinematics Analysis and Simulation of a 5 DOF Robotic Arm using MATLAB
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Kinematics is the mechanics branch which dealswith the movement of the bodies without taking the force into account. In robots, the forward kinematics and inverse kinematics are important in determining the position and orientation of the end-effector to perform multi-tasks. This paper presented the inverse kinematics analysis for a 5 DOF robotic arm using the robotics toolbox of MATLAB and the Denavit-Hartenberg (D-H) parameters were used to represent the links and joints of the robotic arm. A geometric approach was used in the inverse kinematics solution to determine the joints angles of the robotic arm and the path of the robotic arm was divided into successive lines to accomplish the required tasks of the robotic arm.Therefore, this

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Publication Date
Wed Mar 30 2011
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
ESTIMATION OF MASS TRANSFER COEFFICIENTS IN A PACKED DISTILLATION COLUMN USING BATCH MODE
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This research adopts the estimation of mass transfer coefficient in batch packed bed distillation column as function of physical properties, liquid to vapour molar rates ratio (L / V), relative volatility (α), ratio of vapour and liquid diffusivities (DV / DL), ratio of vapour and liquid densities (ρV / ρL), ratio of vapour and liquid viscosities (μV/ μL).
The experiments are done using binary systems, (Ethanol Water), (Methanol Water), (Methanol Ethanol), (Benzene Hexane), (Benzene Toluene). Statistical program (multiple regression analysis) is used for estimating the overall mass transfer coefficient of vapour and liquid phases (KOV and KOL) in a correlation which represented the data fairly well.

KOV = 3.3 * 10-10

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Publication Date
Thu Sep 06 2018
Journal Name
Al-khwarizmi Engineering Journal
Performance Augmenting of a Vertical Axis Wind Turbine using Adaptable Convergent Ducting System
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Developments are carried out to enhance the performance of vertical axis wind turbines (VAWT). This paper studies the performance of the ducted wind turbine with convergent duct (DAWT). Basically, the duct technique is utilized to provide the desired wind velocity facing the turbine. Methodology was developed to estimate the decisive performance parameter and to present the effect of the convergent duct with different inlet angles. The ducted wind turbine was analyzed and simulated using MATLAB software and numerically using ANSYS-Fluent 17.2. Result of both approaches were presented and showed good closeness for the two cases of covering angles 12  and 20 respectively. Results also showed that the convergent duct with an inlet angl

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