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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
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A Comparison Between the Theoretical Cross Section Based on the Partial Level Density Formulae Calculated by the Exciton Model with the Experimental Data for (_79^197)Au nucleus
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In this paper, the theoretical cross section in pre-equilibrium nuclear reaction has been studied for the reaction  at energy 22.4 MeV. Ericson’s formula of partial level density PLD and their corrections (William’s correction and spin correction) have been substituted  in the theoretical cross section and compared with the experimental data for  nucleus. It has been found that the theoretical cross section with one-component PLD from Ericson’s formula when  doesn’t agree with the experimental value and when . There is little agreement only at the high value of energy range with  the experimental cross section. The theoretical cross section that depends on the one-component William's formula and on-component corrected to spi

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Mon Sep 23 2019
Journal Name
Baghdad Science Journal
New Approach for Solving Three Dimensional Space Partial Differential Equation
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This paper presents a new transform method to solve partial differential equations, for finding suitable accurate solutions in a wider domain. It can be used to solve the problems without resorting to the frequency domain. The new transform is combined with the homotopy perturbation method in order to solve three dimensional second order partial differential equations with initial condition, and the convergence of the solution to the exact form is proved. The implementation of the suggested method demonstrates the usefulness in finding exact solutions. The practical implications show the effectiveness of approach and it is easily implemented in finding exact solutions.

       Finally, all algori

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Publication Date
Fri Aug 10 2018
Journal Name
In Book: Challenges In Mechanics Of Time-dependent Materials, Volume 2edition: 1stchapter: 11
A Case Study to Evaluate Live Load Distributions for Pre-stressed RC Bridge
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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
A theoretical Design of a cover for lowering the solar cells temperature and enhance their performance
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In this research, main types of optical coatings are presented which are used as covers for solar cells, these coatings are reflect the infrared (heat) from the solar cell to increase the efficiency of the cell (because the cell’s efficiency is inversely proportional to the heat), then the theoretical and mathematical description of these optical coatings are presented, and an optical design is designed to meet this objective, its optical transmittance was calculated using (MATLAB R2008a) and (Open Filters 1.0.2) programs

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Publication Date
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating Quality of Control Policies and Procedures for Banking Transactions Using the Non-application Gap Model to Enhance Financial Reporting Requirements Applied Study in an Iraqi Private Bank
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The research aims to enhance the level of evaluation of the performance of banking transactions control policies and procedures. The research is based on the following hypothesis: efficient transactions control policies and procedures contribute enhancing financial reporting, by assessing non-application gap of those policies and procedures in a manner that helps to prevent, discover, and correct material misstatementsThe researchers designed an examination list that includes the control policies and procedures related to the transactions, as a guide to the bank audit program prepared by the Federal Financial Supervision Bureau. The research methodology is

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Publication Date
Wed Mar 15 2023
Journal Name
Al-academy
Geometrical Foundations of Shape in Structural Design of Contemporary Ceramic Pots "The artist "IBRAHIM SAEED" is a model"
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Each era has advantages in terms of innovation and development in form, technology, style, and design in ceramic vessels, both at the level of functional and aesthetic performance, so this study aimed to demonstrate the importance of geometrical foundations in the design structure of contemporary ceramic vessels, and also to reveal the constructive skills in The structure of the ceramic figure.
The researchers used the descriptive analytical approach to suit the nature of the study, and they described and analyzed the ceramic works in terms of geometric shape systems, elements and foundations of design in construction, formal diversity in the general design of ceramic vessels, and references and sources of artwork. In addition to th

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Publication Date
Thu Jan 23 2025
Journal Name
Научный форум
PHRASEOLOGISMS RELATED TO THE USE OF COLORS IN SPEECH AS A MEANS OF ENRICHING MODERN RUSSIAN LANGUAGE
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The paper examines key aspects of the use of phraseologi-cal units related to colors in Russian culture and speech. It explores their role in shaping cultural identity, reflecting national characteristics and men-tality. The study analyzes the frequency and contexts of the use of color-related phraseological units in contemporary speech, as well as the influ-ence of media and literature on their popularization. The author highlights the significance of phraseological units in preserving cultural heritage and fostering a deeper understanding of language and culture.

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Publication Date
Thu Oct 01 2020
Journal Name
Biochemical And Cellular Archives
ISOLATION OF SOME PATHOGENIC BACTERIA FROM STUDENTS’ MAKEUP AS A PART OF BIOSAFETY IN THE MEDICAL LABORATORIES
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The bacterial contamination of lipsticks and face cream may become a great important matter in the medical laboratories. The present study was designed to determine the types of bacterial contamination in the face cream and lipsticks of undergraduate students. Also, the study aimed to determine the sensitivity of the isolated bacteria against many antibacterial agents. The study included 190 swabs samples from 190 face cream and lipsticks samples of the females’ students from five departments in the Medical Technology Institute, Almansour, Middle Technical University were collected in February 2018. The swab samples were collected with sterile condition and cultured on enriched Blood agar and MacConkey agar. Serial dilutions were made up

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