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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 Jan 01 2023
Journal Name
Journal Of Pakistan Association Of Dermatologists
The role of epigenetics in immunosuppression in patients with infectious diseases as a fascinating applied observation
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Publication Date
Mon May 31 2021
Journal Name
Iraqi Geological Journal
Mechanical Rock Properties Estimation for Carbonate Reservoir Using Laboratory Measurement: A Case Study from Jeribe, Khasib and Mishrif Formations in Fauqi Oil Field
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Estimation of mechanical and physical rock properties is an essential issue in applications related to reservoir geomechanics. Carbonate rocks have complex depositional environments and digenetic processes which alter the rock mechanical properties to varying degrees even at a small distance. This study has been conducted on seventeen core plug samples that have been taken from different formations of carbonate reservoirs in the Fauqi oil field (Jeribe, Khasib, and Mishrif formations). While the rock mechanical and petrophysical properties have been measured in the laboratory including the unconfined compressive strength, Young's modulus, bulk density, porosity, compressional and shear -waves, well logs have been used to do a compar

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Publication Date
Tue Dec 24 2024
Journal Name
Malaysian Journal Of Mathematical Sciences
Exploring the Role of Hunting Cooperation, and Fear in a Prey-Predator Model with Two Age Stages
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The aim of this study is to utilize the behavior of a mathematical model consisting of three-species with Lotka Volterra functional response with incorporating of fear and hunting cooperation factors with both juvenile and adult predators. The existence of equilibrium points of the system was discussed the conditions with variables. The behavior of model referred by local stability in nearness of any an equilibrium point and the conditions for the method of approximating the solution has been studied locally. We define a suitable Lyapunov function that covers every element of the nonlinear system and illustrate that it works. The effect of the death factor was observed in some periods, leading to non-stability. To confirm the theore

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Publication Date
Mon Jun 15 2020
Journal Name
Al-academy
Religious references to art of miniatures In the Iranian school (Behzad is a model): عبدالرزاق جبار رحيل
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The study examines the religious references of the art of miniatures in the Iranian school "Bahzad model" completed in Iran during the twelfth century AH, according to the controls and characteristics of the authoritative references. The researcher presented the problem of research, its importance, the need for it and its purpose, defined the terms in the research. The theoretical framework came with three investigations. The first topic of the concept of the reference in the field of knowledge, which concluded the most important features of the reference, is that each symbolic existence corresponds to a real existence and symbolic presence is an input to the realization of the reference. The reference then becomes a sign that acts as a

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Publication Date
Tue Jan 21 2025
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A comparison between the hierarchical clustering methods for postgraduate students in Iraqi universities for the year 2019-2020 using the cophenetic and delta correlation coefficients
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The educational sector is one of the important sectors in the world, and it is considered one of the means of community development. In addition, it is one of the means of making the country’s renaissance and devel-opment because it represents the factory of thinking minds that make change. There is no doubt that this sector is the same as any other sector. The deficit in the studied scientific planning has been prolonged, which led to its deterioration, and the problems of education remain diverse and inherited from previous time periods, where the hierarchical cluster analysis was used on postgraduate students in universities in Iraq, except for Kurdistan region, and the number of universities that were included in the study was

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Publication Date
Mon Jan 01 2018
Journal Name
Research Journal Of Pharmacy And Technology
Molecular Genetic variability in the D-loop region for females with Breast Cancer and the effect of the Chemotherapy
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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
A Comparative Investigation of Different Ionospheric Models to Predict the MUF Parameter During Severe Geomagnetic Storm on 17th March 2015.
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The present work aimed to make a comparative investigation between three different ionospheric models: IRI-2020, ASAPS and VOACAP. The purpose of the comparative study is to investigate the compatibility of predicting the Maximum Usable Frequency parameter (MUF) over mid-latitude region during the severe geomagnetic storm on 17 March 2015. Three stations distributed in the mid-latitudes were selected for study; these are (Athens (23.50o E, 38.00o N), Jeju (124.53o E, 33.6o N) and Pt. Arguello (239.50o W, 34.80o N). The daily MUF outcomes were calculated using the tested models for the three adopted sites, for a span of five-day (the day of the event and two days preceding and following the event day). The calculated datasets were co

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Publication Date
Sun Jun 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The economic effects of money laundering and the role of banking service in combat it: a prospective study of a sample
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Money laundering is consider a crime in legal perspective and aphenomenon of negative effects in economic and Social perspective for thevarious countries of the world by the diversity of their economies to make thebadly damaged in the banking service and its reputation in some cases may leadto bankruptcy of banks, and the fact that banks is one of the most importantcircles that revolve the illicit funds, Due to its branched the banking operations,speed and overlap and increase it's complicated with the progress of bankingoperations and the use of electronic services modern here's challenges atvarious levels between the application of the legislation to combat moneylaundering and between actual fact it must find ways and means of legislat

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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Role of the values of accounting culture in maximizing financial performance - A field study in a sample of Iraqi banks
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The influence of culture on accounting systems and practices, including financial reports and accounting information through the values ​​identified by Gray and derived from social-cultural values, and the four accounting values ​​were derived from generally accepted accounting principles represented by (Conservatism, Uniformity, Secrecy, and Professionalism). Important and significant in maximizing financial performance, and measuring the extent of the role of these values ​​in improving financial performance through attention to the values ​​of accounting culture, this research

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Publication Date
Wed Dec 30 2009
Journal Name
Iraqi Journal Of Physics
Study the Effect of annealing temperature on the Structure of a-Se and Electrical Properties of a-Se/c-Si Heterojunction
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In this work Study effect of annealing temperature on the Structure
of a-Se and electrical properties of a-Se/c-Si hetrojunction have been
studied.The hetrojunction fabricated by deposition of a-Se film on c-
Si using thermal evaporation.
Electrical properties of a-Se/ c-Si heterojunction include I-V
characteristics, in dark at different annealing temperature and C-V
characteristics are considered in the present work.
C-V characteristics suggested that the fabricated diode was
abrupt type, built in potential determined by extrapolation from
1/C2-V curve. The built - in potential (Vbi) for the Se/ Si System
was found to be increase from 1.21 to 1.62eV with increasing of
annealing temperature

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