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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 Jun 01 2021
Journal Name
Journal Of The College Of Languages (jcl)
The Construction of a National Identification in the Novel of N. Scott Momaday House Made of Dawn
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The United States government allowed Native Americans to abandon their reservations in the 1950s and 1960s. The historical, social, and cultural backgrounds shaped the forms and themes of works by American Indian writers who urged people to refuse their culture's sense of shame. Moreover, their behavior corresponded with the restoration of individuals to their rituals after disappointment, loss of sense of life, and mental illness performed from the influence of mainstream American society. Among these writers, N. Scott Momaday and Leslie Marmon Silko participate in similar interest in portraying characters caught between indigenous beliefs and white mainstream standards.  

      The construction of

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Publication Date
Sun Jun 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
The Exploitation of Carmen Valero Garces' Theory in the Criticism of Literary Texts: Saleh al-Jafari's Arabic Translation of "Rubbayat al-Khayyam" as a: کاربست نظریه¬ی کارمن والرو گارسس در نقد ترجمه¬ی ادبی (مورد مطالعه: تعریب صالح الجعفری از رباعیات خیام)
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There is a mutual relationship between the form of a text and its meaning so as separating these two or devaluating the role of one of them leads to the absence of the value therein. Thus, a translation is important as to how it relates the details of a text. That is, the text has special features which go beyond form, and these set out its distinctiveness. Here, we tackle Saleh al-Jafari's Arabic translation of  "Rubbayat al-Khayyam" of Naysapour descriptively and analytically by depending on extracts from the original text. This translation is evaluated on the basis of Spanish critic Maria Carmen Valero Garces. Herein, we discuss the effectiveness of this theory in the criticism of literary texts. It has been concluded that al-Jaf

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
The Effect of Woods model in the Acquisition of Grammatical Concepts on students at the Sixth primary
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The research aims at identifying The Effect of Woods model in the Acquisition of Grammatical Concepts on students at the Sixth Primary. The total number of students is (49) male and female. students are distributed in two groups . The First group is the experimental group which is taught the( Woods Model) and it is (25) students . The second group is the control group which is taught according to the traditional method of teaching and it is (24) students . The researcher has matched between the two groups by the following variables : the age (in months), their intelligence, their parents, academic level of education . The research has constructed multiple choice test of (20) items . The reliability of The test has been calculated and it

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Publication Date
Sun Sep 04 2011
Journal Name
Baghdad Science Journal
The Prediction of the Electromagnetic Properties and the ?(E2/M1) of 110-116Cd-Isotopes in IBM Model
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The Nuclear structure of 110-116Cd isotopes was studied theoretically in the framework of the interacting boson model of IBM-l and IBM-2. The properties of the lowest mixed symmetry states such as the 1+, 2+ and 3+ levels produced by the IBM-2 model in the vibrational-limit U(5) of Cd - isotopes are studied in details. This analysis shows that the character of mixed symmetry of 2+ is shared between and states in 110-114Cd – isotopes, the large shar goes to s, while in isotope, the state is declared as a mixed symmetry state without sharing. This identification is confirmed by the percentage of F-spin contribution. The electromagnetic properties of E2 and Ml operators were investigated and the results were analyzed. Various

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Publication Date
Thu Sep 30 2021
Journal Name
Iraqi Journal Of Science
The Dynamics of Sokol-Howell Prey-Predator Model Involving Strong Allee Effect
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In this paper,  a Sokol-Howell prey-predator model involving strong Allee effect is proposed and analyzed. The existence, uniqueness, and boundedness are studied. All the five possible equilibria have been are obtained and their local stability conditions are established. Using Sotomayor's theorem, the conditions of local saddle-node and transcritical and pitchfork bifurcation are derived and drawn. Numerical simulations are performed to clarify the analytical results

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Publication Date
Tue Jan 02 2018
Journal Name
Journal Of Educational And Psychological Researches
The effect of Dunn Dunn model on students’ achievement in Geography course
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The study seeks to investigate the effect of Dunn Dunn learning style model on students’ achievement. Besides, the way of developing students’ deductive thinking by testing the null hypothesis: there is no significant difference between experimental group who takes Dunn Dunn model as style in studying geography and control group that follows a traditional method in studying geography at the level of (0,05). Additionally, there is no significant difference between experimental group who takes Dunn Dunn model as style in studying geography and control group that follows a traditional method in studying geography at the level of (0,05) on testing developing deductive thinking skills. The researcher adopted a quasi-experimental posttest

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Publication Date
Tue Jul 01 2025
Journal Name
Mastering The Minds Of Machines
The Impact of Transfer Learning and Pre-trained Models on Model Performance
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Publication Date
Sun Jul 30 2023
Journal Name
Iraqi Journal Of Science
Estimation of the Standard Atmospheric Earth Model Parameters at 86 km Altitude
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     Utilizing the Turbo C programming language, the atmospheric earth model is created from sea level to 86 km. This model has been used to determine atmospheric Earth parameters in this study. Analytical derivations of these parameters are made using the balancing forces theory and the hydrostatic equation. The effects of altitude on density, pressure, temperature, gravitational acceleration, sound speed, scale height, and molecular weight are examined. The mass of the atmosphere is equal to about 50% between sea level and 5.5 km. g is equal to 9.65 m/s2 at 50 km altitude, which is 9% lower than 9.8 m/s2 at sea level. However, at 86 km altitude, g is close to 9.51 m/s2, which is close to 15% smaller than 9.8 m/s2.  These resu

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Publication Date
Fri Mar 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Improving the Effectiveness of Internal Control System In Accordance with COSO Model
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        The research aims to improve the effectiveness of internal control system according to a model COSO, by identifying the availability of system components according to the model and then improve the effectiveness of each component by focusing on areas for improvement in each component, as it was addressed to a model COSO and then Maamth with the environment, the current Iraqi by introducing some improvements on the form of some mechanisms of corporate governance of the Council of Directors, and senior management, the Audit Committee, Committee appointments, especially that supplies application available in the laws and legislation, the current Iraqi, taking into consideration to make some

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Publication Date
Fri Jun 23 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
The dynamic of an eco-epidemiological model involving fear and hunting cooperation
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In the present paper, an eco-epidemiological model consisting of diseased prey consumed by a predator with fear cost, and hunting cooperation property is formulated and studied. It is assumed that the predator doesn’t distinguish between the healthy prey and sick prey and hence it consumed both. The solution’s properties such as existence, uniqueness, positivity, and bounded are discussed. The existence and stability conditions of all possible equilibrium points are studied. The persistence requirements of the proposed system are established. The bifurcation analysis near the non-hyperbolic equilibrium points is investigated. Numerically, some simulations are carried out to validate the main findings and obtain the critical values of th

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