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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 Jul 02 2017
Journal Name
Iraqi Journal Of Science
A Study Medicinal and Nutritional Effects of Thyme on Hematological Changes in Male Albino Rats
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Publication Date
Fri Nov 22 2019
Journal Name
Chalcogenide Letters
CONCENTRATION EFFECTS ON ELECTRONIC AND SPECTROSCOPIC PROPERTIES OF ZnCdS WURTZOIDS: A DENSITY FUNCTIONAL THEORY STUDY
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Publication Date
Thu May 28 2020
Journal Name
Journal Of Generic Medicines: The Business Journal For The Generic Medicines Sector
Determinants of national drug products acceptance across patients, pharmacists, and manufacturers: A mixed method study
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Introduction

The national pharmaceutical industry is pivotal for both the health sector and the national economy. This study aims to identify determinants of national drug products acceptance. The objectives of this study were to quantitatively measure the level of patient and community pharmacist acceptance of national drug products available in community pharmacies and to qualitatively explore the barriers facing national pharmaceutical companies and investigate the suggested solutions.

Methods

This cross-sectional study used an explanatory mixed method design. It was conducted in Baghdad, Iraq from July through October 2018. The stud

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Publication Date
Fri Apr 01 2022
Journal Name
Heliyon
Stigma towards health care providers taking care of COVID-19 patients: A multi-country study
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Publication Date
Sat Sep 12 2020
Journal Name
Al-kindy College Medical Journal
Spectrum of central nervous system infections in neurosciences hospital in two years : a retrospective study
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Background :Infectious disorders in general have high morbidity and mortality.. CNS infections include many disorders like bacterial meningitis, tuberculous and other subacute and chronic meningitis, viral meningitis, cerebral abscess, spinal cord infections, and others.
Objective: To assess our locality about prevalence of CNS infections , to have more awareness regarding CNS infections, and to try to find the proper way to reduce their prevalence and to treat them in appropriate way.
Method :We revised the records of all the cases of CNS infections excluding cases of spinal cord infections who were admitted in the wards of neuroscience hospital over the previous two years ( from July/2010 to June 2012 ),those were 132 cases.Seaso

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Publication Date
Sat Jan 01 2011
Journal Name
Al-mustansiriyah Journal Of Science
TMA and DSC study of molded and annealed polyester: a thermal expansion and crystallization evaluation
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Thermomechanical analysis (TMA) and differential scanning calorimetry (DSC) are used to investigate the effect of molding and annealing of polyester on the behavior of thermal expansion and crystallization since these factors play role in the reprocessing or recycling of the polymer. The dynamic mode of the TMA provides enhanced characterization information about the polyester since it separates the transitions into reversible and irreversible signals, and also reveals the progress of the amorphous regions as the polyester loses strength with the increasing temperature approaching melting. Slow cooling after annealing brings crystallization that may be attributed to molecular chain straightening due to orientation.

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Publication Date
Tue Oct 07 2003
Journal Name
University Of Baghdad
A STUDY ON SOLVENT EXTRACTION OF HOLMIUM (III) WITH SUDAN BLACK B REAGENT (M.Sc. Thesis)
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Publication Date
Fri Sep 02 2022
Journal Name
Frontiers In Built Environment
Thermal analysis of horizontal earth-air heat exchangers in a subtropical climate: An experimental study
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The earth-air heat exchanger (EHX) has a promising potential to passively save the energy consumption of traditional air conditioning systems while maintaining a high degree of indoor comfort. The use of EHX systems for air conditioning in commercial and industrial settings offers several environmental benefits and is capable of operating in both standalone and hybrid modes. This study tests the performance and effectiveness of an EHX design in a sandy soil area in Baghdad, Iraq. The area has a climate of the subtropical semi-humid type. Ambient air temperatures and soil temperatures were recorded throughout the months of 2021. During the months of January and June, the temperatures of the inlet and outflow air at varying air veloci

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Publication Date
Sun May 12 2019
Journal Name
Al-khwarizmi Engineering Journal
Motion Control of Three Links Robot Manipulator (Open Chain) with Spherical Wrist
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Robot manipulator is a multi-input multi-output system with high complex nonlinear dynamics, requiring an advanced controller in order to track a specific trajectory. In this work, forward and inverse kinematics are presented based on Denavit Hartenberg notation to convert the end effector planned path from cartesian space to joint space and vice versa where a cubic spline interpolation is used for trajectory segments to ensure the continuity in velocity and acceleration.  Also, the derived mathematical dynamic model is based on Eular Lagrange energy method to contain the effect of friction and disturbance torques beside the inertia and Coriolis effect. Two types of controller are applied ; the nonlinear computed torque control (CTC

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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Bacterial and Fungal Contamination in Three Brands of Cosmetic Marketed in Iraq
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         Cosmetic products must be safe for use by consumers , It is also regulated and required the legislation of countries all over the world .  In this study out of 80 cosmetic products analyzed and 32.5% were found to be contaminated .Products such as mascara, lip pencil and eye pencil were analyzed . The contaminants including bacteria such as Staphylococcus aureus , Staphylocoocus epidermidis , Pseudomonas aeruginosa , Escherichia coli and Klebsiella pneumonia   which were ranging  in number  from (103-104 ) C.F.U. /ml and fungi such as Penicillium spp. , <

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