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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 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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Publication Date
Tue May 17 2016
Journal Name
Iosr Journal Of Nursing A Nd Health Science (iosr-jnhs)
Comparative Study of Abnormal Renal Function Tests and Liverfunction Tests in Type1 and Type2 Diabetes Mellitus in Iraq
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This study was planned to evaluate the renal function tests and liver function tests and it carried out in Al-Yarmouk hospital,Baghdad –Iraqin patients withtype 1 and type 2 diabetes mellitus by measuring(uric acid,urea and creatinine) ,Aspartate aminotransferase (AST) and Alanine aminotransferase (ALT). Seventy five individuals of Iraqi adults (male) were divided into three groups, 25 patients with type1 diabetes mellitus ,25 patients with type 2 diabetes mellitus and 25 normal individuals were taken as control group. The mean value of uric acid, urea and creatinine was higher significantly in patients thanin control group (P< 0.05),while the correlation(p< 0.01) between age ,creatinine in type 1 and between age and (Urea, Uric acid ,cr

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Publication Date
Fri Feb 25 2022
Journal Name
Open Access Macedonian Journal Of Medical Sciences
Prospective Comparative Study of Fixing Displaced Transverse Patellar Fracture by Tension Band Wiring Versus Cannulated Screws with Wiring
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BACKGROUND: Transverse fractures of the patella are important fractures with a wide variety of subtypes, the common incidence in the age group of 20–50 years. Surgical interference aims to achieve a perfect alignment of the joint surface, in addition to rigid fixation of the fracture for early re-habitation and early movement to retain the extensor mechanism of the knee joint. AIM: The aim of this study was to compare the radiological and functional outcomes of the displaced transverse patella fracture in adult patients treated by ORIF using tension band wiring versus cannulated screws with wiring. METHODS: A prospective analytic comparative study was conducted in Al-Kindy Teaching Hospital/Baghdad/Iraq for 18 months from Apr

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Publication Date
Mon Dec 18 2017
Journal Name
Al-khwarizmi Engineering Journal
Comparative Study of Performance and Emission Characteristics between Spark Ignition Engine and Homogeneous Charge Compression Ignition Engine (HCCI)
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Many researchers consider Homogeneous Charge Compression Ignition (HCCI) engine mode as a promising alternative to combustion in Spark Ignition and Compression Ignition Engines. The HCCI engine runs on lean mixtures of fuel and air, and the combustion is produced from the fuel autoignition instead of ignited by a spark. This combustion mode was investigated in this paper. A variable compression ratio, spark ignition engine type TD110 was used in the experiments. The tested fuel was Iraqi conventional gasoline (ON=82).

The results showed that HCCI engine can run in very lean equivalence ratios. The brake specific fuel consumption was reduced about 28% compared with a spark ignition engine. The experimental tests showed that the em

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Marginal leakage of amalgam and modern composite materials related to restorative techniques in class II cavity (Comparative study)
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Background: Restoration of the gingival margin of Class II cavities with composite resin continues to be problematic, especially where no enamel exists for bonding to the gingival margin. The aim of study is to evaluate the marginal leakage at enamel and cementum margin of class II MOD cavities using amalgam restoration and modern composite restorations Filtek™ P90, Filtek™ Z250 XT (Nano Hybrid Universal Restorative) and SDR bulk fill with different restoratives techniques. Materials and method: Eighty sound maxillary first premolar teeth were collected and divided into two main groups, enamel group and cementum group (40 teeth) for each group. The enamel group was prepared with standardized Class II MOD cavity with gingival margin (1 m

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the effect of Autolougues Platelet Rich Fibrin Matrix on osseointegration of the titanium implant immunohistochemical evaluation for PDGF-I&IGF-A
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Background: Platelet-rich fibrin (PRF) is a simple, low cost and minimally invasive way to obtain a natural concentration of autologous growth factors and is currently being widely experimented in different fields of medicine for its ability to aid the regeneration of tissue with a low healing potential. Fields of application are sports medicine, orthopedics, dentistry, dermatology, ophthalmology, plastic and maxillofacial surgery, etc. The rationale for using platelets in so many fields for the treatment of different tissues is because PLTs constitute a reservoir of critical GFs and cytokines, which may govern and regulate the tissue healing process that is quite similar in all kinds of tissues. Materials and Methods: Screw titanium implan

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Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
Study of electron energy distribution function and transport parameters for CF4 and Ar gases discharge by using the solution of Boltzmann equation-Part I
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The Boltzmann transport equation is solved by using two- terms approximation for pure gases . This method of solution is used to calculate the electron energy distribution function and electric transport parameters were evaluated in the range of E/N varying from . 172152110./510.VcmENVcm
From the results we can conclude that the electron energy distribution function of CF4 gas is nearly Maxwellian at (1,2)Td, and when E/N increase the distribution function is non Maxwellian. Behavior of electrons transport parameters is nearly from the experimental results in references. The drift velocity of electron in carbon tetraflouride is large compared with other gases

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Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
Study of electron energy distribution function and transport parameters for CF4, Ar gases mixture discharge by using the solution of Boltzmann equation-Part II
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The Boltzmann transport equation is solved by using two- terms approximation for pure gases and mixtures. This method of solution is used to calculate the electron energy distribution function and electric transport parameters were evaluated in the range of E/N varying from . 172152110./510.VcmENVcm
The electron energy distribution function of CF4 gas is nearly Maxwellian at (1,2)Td, and when E/N increase the distribution function is non Maxwellian. Also, the mixtures are have different energy values depending on transport energy between electron and molecule through the collisions. Behavior of electrons transport parameters is nearly from the experimental results in references. The drift velocity of electron in carbon tetraflouride i

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Publication Date
Fri Apr 12 2019
Journal Name
Journal Of Economics And Administrative Sciences
Comparative Development between the Asian Tiger Crisis and the Mortgage Crisis
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Financial crisis is one of the topics that have attracted the interest of researchers in recently. The research focused on the issue of the crisis of the Asian Tigers and the mortgage crisis and comparing them in terms of causes and repercussions. It may meet most of the financial crises in many of its causes, factors, roots and results in the advanced and the developing countries. This crisis has its own pattern and its causes and nature and it is characterized by a crisis of cash liquidity and the collapse of many banks and declare bankruptcy and a sharp decline in stock prices and indices of the stock market and so far the common denominators among the causes but does not mean this There are differences between the financial c

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