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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
Tue Apr 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Developing a Learning Organization According to Analysis of the Relationship between Knowledge Gap and Strategic Performance Gaps: Field Study in a Sample of Private Banks in Baghdad.
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The purpose of this research shed light on the analysis of the relationship between the knowledge gap and the strategic performance  gap and diagnose the level of impact this relationship in building a learning organization, and sought search to achieve a number of goals, cognitive and Applied been tested nature of the relationship and effect between variables in a sample size (62) of the managers of banks civil in Baghdad (Baghdad, Gulf, Assyria, Union, Elaf) and focused research problem in question is bold is whether the analysis of the relationship between the knowledge gap and the performance gap strategic leads to recognize organizations need to shift to organizations educated, either in the side of the field was the pr

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Publication Date
Sat Jan 27 2024
Journal Name
History Of Medicine
Developing and Validating a Spectrophotometric Method for Estimating Antifungal (Nystatin) in its Pure Form Pharmaceutical Formulation Using Tetrachloro-1,4 benzoquinone
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The UV−VIS absorption spectroscopy technique was used to study the formation of a new complex of charge transfer (CT) between bioactive organic molecules as (Nystatin) containing both a π-electrons from a conjugated system and lone-pair of electrons (amine) with Tetrachloro-1,4 benzoquinone (TCBQ) as a π-acceptor in which the transferred electron goes into its vacant anti-bonding molecular orbitals. The Tyrian purple-colored complex formed was quantitatively measured at 544 nm. This complex shows obeying Beer's law within the concentration range of (10-90) μg.ml-1The stoichiometry of the formed complex between the (Nys.) and (TCBQ) was found 1:2 as evaluated by continuous variation (Job's method) and mole ratio method The value of mola

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Publication Date
Tue Jul 09 2024
Journal Name
Diagnostics
A Novel Hybrid Machine Learning-Based System Using Deep Learning Techniques and Meta-Heuristic Algorithms for Various Medical Datatypes Classification
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Medicine is one of the fields where the advancement of computer science is making significant progress. Some diseases require an immediate diagnosis in order to improve patient outcomes. The usage of computers in medicine improves precision and accelerates data processing and diagnosis. In order to categorize biological images, hybrid machine learning, a combination of various deep learning approaches, was utilized, and a meta-heuristic algorithm was provided in this research. In addition, two different medical datasets were introduced, one covering the magnetic resonance imaging (MRI) of brain tumors and the other dealing with chest X-rays (CXRs) of COVID-19. These datasets were introduced to the combination network that contained deep lea

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Prediction of the Effect of Using Stone Column in Clayey Soil on the Behavior of Circular Footing by ANN Model
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Shallow foundations are usually used for structures with light to moderate loads where the soil underneath can carry them. In some cases, soil strength and/or other properties are not adequate and require improvement using one of the ground improvement techniques. Stone column is one of the common improvement techniques in which a column of stone is installed vertically in clayey soils. Stone columns are usually used to increase soil strength and to accelerate soil consolidation by acting as vertical drains. Many researches have been done to estimate the behavior of the improved soil. However, none of them considered the effect of stone column geometry on the behavior of the circular footing. In this research, finite ele

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Publication Date
Wed Apr 14 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Estimation of domestic urban electricity consumption: A case study of Baghdad, Iraq
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Electricity consumption for household purposes in urban areas widely affects the general urban consumption compared to other commercial and industrial uses, as household electricity consumption is affected by many factors related to the physical aspects of the residential area such as temperature, housing unit area, and coverage ratio, as well as social and economic factors such as family size and income, to reach the extent of the influence of each of the above factors on the amount of electricity consumed for residential uses, a selected sample of a residential area in the city of Baghdad was studied and a field survey conducted of the characteristics of that sample and the results analyzed and modeled statistically in relation to the amo

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Publication Date
Tue Jun 01 2021
Journal Name
Iraqi Journal Of Physics
A Study of Crystallographic and DC Electrical Characteristics of PPy/Ag Nanocomposites
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ABSTRACT: Polypyrrole and polypyrrole / silver nanocomposites were fabricated by in-situ polymerization employing Ammonium Persulphate as an oxidizing agent. Nanocomposites were synthesized by combining polypyrrole and silver nanoparticles in various weight percentages (0.1%, 0.5%, 3%, 5% and 7% wt.). Crystallographic data were collected using X-ray diffraction.  PPy particles were found to have an orthorhombic symmetry. In contrast, PPy/Ag nanocomposites were reported to have monoclinic structure. The crystallite size was determined by XRD using Scherrer equation and considered to be within 49 nm range. DC conductivity of pelletized samples was evaluated in the temperature range of 323.15k to 453.15k. The conductiv

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Publication Date
Tue Jun 01 2021
Journal Name
Iraqi Journal Of Physics
A Study of Crystallographic and DC Electrical Characteristics of PPy/Ag Nanocomposites
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ABSTRACT: Polypyrrole and polypyrrole / silver nanocomposites were fabricated by in-situ polymerization employing Ammonium Persulphate as an oxidizing agent. Nanocomposites were synthesized by combining polypyrrole and silver nanoparticles in various weight percentages (0.1%, 0.5%, 3%, 5% and 7% wt.). Crystallographic data were collected using X-ray diffraction.  PPy particles were found to have an orthorhombic symmetry. In contrast, PPy/Ag nanocomposites were reported to have monoclinic structure. The crystallite size was determined by XRD using Scherrer equation and considered to be within 49 nm range. DC conductivity of pelletized samples was evaluated in the temperature range of 323.15k to 453.15k. The conductivity displayed an

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Publication Date
Thu Jun 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Customers emotional blackmail and reduce it the new product- study of the opinions of a sample of customers who deal with peak economy for household items in najaf al Ashraf
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The challenges facing today's multi-customer and this is due to the multiplicity of products and speed in launching new products so search came to reveal the  reveal the of the new product classification standards through a relationship (good products, low interest products, useful products and products desired) and the customer emotionally blackmail through deportation (fear, obligation and guilt). dentified the problem of the research in several questions focused on the nature of the relationship between the variables of research, and for that outline supposedly to search it expresses the head of one hypothesis and branched out of which four hypotheses subset, but in order to ensure the validity of the ass

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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Semiconductors
Bilayer MSe<sub>2</sub> (M = Zr, Hf, Mo, W) performance as a hopeful thermoelectric materials
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Abstract<p>Significant advancements in nanoscale material efficiency optimization have made it feasible to substantially adjust the thermoelectric transport characteristics of materials. Motivated by the prediction and enhanced understanding of the behavior of two-dimensional (2D) bilayers (BL) of zirconium diselenide (ZrSe<sub>2</sub>), hafnium diselenide (HfSe<sub>2</sub>), molybdenum diselenide (MoSe<sub>2</sub>), and tungsten diselenide (WSe<sub>2</sub>), we investigated the thermoelectric transport properties using information generated from experimental measurements to provide inputs to work with the functions of these materials and to determine the </p> ... Show More
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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
A study in Tunisian - Iraqi Relations and its role in determining strategies for dealing with conflict and peace situations
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If the State attaches great importance to its foreign relations and intends to strengthen them in order to ensure the achievement of the highest national goals and interests. External relations between countries are one of the most prominent features of foreign policy, which depends on a combination of internal and external factors, the modern relations between Tunisia and Tunisia, which goes back to the pre-independence of Tunisia, when Iraq was a supporter of Tunisia's independence from France in the 1940s, Although these relations did not cause any disturbance by the two countries, but they remained weak relations did not develop in all areas except the sports and cultural field, which we will determine the reasons and the pos

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