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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
Fri Jan 01 2016
Journal Name
Journal Of The College Of Languages (jcl)
Linguistic contast between bilateral and trilateral roots in Semitics languages (Arabic and Syriac as a model)
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The present study investigates the relation between the biliteral and triliteral roots which is the introduction to comprehend the nature of the Semitic roots during its early stage of development being unconfirmed to a single pattern. The present research is not meant to decide on the question of the biliteral roots in the Semitic languages, rather it is meant to confirm the predominance of the triliteral roots on these languages which refers, partially, to analogy adopted by the majority of linguists. This tendency is frequently seen in the languages which incline to over generalize the triliteral phenomenon, i. e., to transfer the biliteral roots to the triliteral room, that is, to subject it to the predominant pattern regarding the r

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Publication Date
Sun Jan 24 2016
Journal Name
Al-academy
Babylonian theater (Its history, models and properties) a historical comparative study: محمد صبري صالح
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The building of the Babylonian theater is considered as one of the distinctive buildings where its foundations have remained steadfast in the face of geographical changes, social's erosion and groundwater that threatened almost all traces of Babylon despite the destruction of the outer structure of the building. The general directorate of antiques performed prospection for those foundations (the ground map), and then the building was completed by new bricks over the original scheme. It became clear when examining the building; its components and foundations, that the building is unique in comparison with the old buildings of the world throughout Iraq. There are similar buildings in other places like Jordan and North Africa such as

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Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
A Comparative Study between Transcutaneous Bilirubinometry and Total Serum Bilirubin Measurement in Jaundiced Newborns
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Background: Drawing blood to measure total serum bilirubin is painful & time consuming. Transcutaneous bilirubinometer working by multiwavelength spectral reflectance from the skin surface on forehead or upper sternum is a quick & painless technique. 

Objectives: to compare the effectiveness of transcutaneous (over the upper sternum and forehead) and serum bilirubin measurement of neonate with jaundice.

Subjects and Methods: This is a cross sectional prospective study. It enrolled 175 jaundiced neonates & excluded those exposed to phototherapy. It was conducted at Child Central Teaching Hospi

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Publication Date
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Chronic Tennis Elbow Treated by Platelet-Rich Plasma Versus Steroid Injections: A Comparative Study
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Background: Painful elbow joint over the lateral epicondyle especially with resisted wrist extension are common signs of lateral epicondyle tendinopathy, also called tennis elbow. Objective: To evaluate the clinical outcome of local platelet rich plasma (PRP) injection in patients with chronic tennis elbow compared with a steroid (Depomedrol 40 mg) injection. Methods: A total of 88 patients with chronic tennis elbow were treated at Al-Kindy Teaching Hospital and private clinics. All patients had chronic pain for about 24 weeks or more and had failed first line treatment. The patients dividing into two groups, Group A injected with PRP (n = 44), and group B injected with depomedrol 40 mg (n = 44). A good clinical result w

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Publication Date
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Chronic Tennis Elbow Treated by Platelet-Rich Plasma Versus Steroid Injections: A Comparative Study
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Background: Painful elbow joint over the lateral epicondyle especially with resisted wrist extension are common signs of lateral epicondyle tendinopathy, also called tennis elbow.

Objective: To evaluate the clinical outcome of local platelet rich plasma (PRP) injection in patients with chronic tennis elbow compared with a steroid (Depomedrol 40 mg) injection.

Methods: A total of 88 patients with chronic tennis elbow were treated at Al-Kindy Teaching Hospital and private clinics. All patients had chronic pain for about 24 weeks or more and had failed first line treatment. The patients dividing into two groups, Group A injected with PRP (n = 44), and group B injected with d

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Publication Date
Thu Sep 01 2022
Journal Name
Journal Of Stomatology
The effectiveness of limited flap design in surgical removal of fully impacted lower third molars: a comparative clinical study
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Publication Date
Wed Jul 01 2015
Journal Name
Journal Of Engineering
A comparative Isothermal and Kinetic Study of the Adsorption of Lead (II) from Solution by Activated Carbon and Bentonite
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This work is aiming to study and compare the removal of lead (II) from simulated wastewater by activated carbon and bentonite as adsorbents with particle size of 0.32-0.5 mm. A mathematical model was applied to describe the mass transfer kinetic.

The batch experiments were carried out to determine the adsorption isotherm constants for each adsorbent, and five isotherm models were tested to choose the best fit model for the experimental data. The pore, surface diffusion coefficients and mass transfer coefficient were found by fitting the experimental data to a theoretical model. Partial differential equations were used to describe the adsorption in the bulk and solid phases. These equations were simplified and the

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Publication Date
Sat Jun 21 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Fracture strength of laminate veneers using different restorative materials and techniques (A comparative in vitro stuy)
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Background: Esthetic correction represents one of the clinical conditions that required the use of laminate veneers in premolars region. Aim of the study: The purpose of this study was to evaluate the fracture strength of the laminate veneers in maxillary first premolars, fabricated from either composite (direct and indirect techniques) or ceramic CAD/CAM blocks. Materials and Methods: Fifty sound human maxillary premolar teeth were used in this in vitro study. Teeth were divided randomly into one control group and four experimental groups of ten teeth each; Group A: Restored with direct composite veneer (Filtek Z250 XT), Group B: Restored with indirect composite veneers (Filtek Z250 XT), Group C: Restored with lithium disilicate ceramic CA

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Publication Date
Sun Dec 22 2019
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Ex-vivo Ex-Vivo Absorption Study of a Novel Dabigatran Etexilate Loaded Nanostructured Lipid Carrier Using Non-Everted Intestinal Sac Model
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Abstract

The purpose of our study was to develop Dabigatran Etexilate loaded nanostructured lipid carriers (DE-NLCs) using Glyceryl monostearate and Oleic acid as lipid matrix, and to estimate the potential of the developed delivery system to improve oral absorption of low bioavailability drug, different Oleic acid ratios effect on particle size, zeta potential, entrapment efficiency and loading capacity were studied, the optimized DE-NLCs shows a particle size within the nanorange, the zeta potential (ZP) was 33.81±0.73mV with drug entrapment efficiency (EE%) of  92.42±2.31% and a loading capacity (DL%) of 7.69±0.17%. about 92% of drug was released in 24hr in a controlled manner, the ex-vivo intestinal p

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Publication Date
Tue Sep 01 2020
Journal Name
Journal Of Engineering
Optimization and Modeling the Performance of a Mediator-less Microbial Fuel Cell using Butler-Volmer-Monod Model
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In this study, a one-dimensional model represented by Butler-Volmer-Monod (BVM) model was proposed to compute the anode overpotential and current density in a mediator-less MFC system. The system was fueled with various organic loadings of real field petroleum refinery oily sludge to optimize the favorable organic loading for biomass to operate the suggested system. The increase in each organic loading showed higher resistance to electrons transport to the anode represented by ohmic loss. On the contrary, both activation and mass transfer losses exhibited a noticeable decrement upon the increased organic loadings. However, current density was improved throughout all increased loads achieving a maximum current density of 5.2 A/m3

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