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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 Mar 31 2020
Journal Name
College Of Islamic Sciences
(Novelist character in the Iraqi press criticism – Fadhil Thamir as a model))
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Novel has recently  received the attention of readers and writers greatly, because of the role they play, and this indicates an important rule, which is whenever there is an art or creativity, there must be a respective criticism, and this criticism is certainly not less important than the author. So there are critics who have a prestigious literary position in the follow-up story development, and trying to describe the transformation of its elements. One of these critics is professor Fadhel Thamer, and who wants to approach one of the elements of the novel exploring, must stop on the visions of this critic about it , and that’s why we take the (character) element following the most important opinions of this critic about

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Publication Date
Fri Dec 01 2023
Journal Name
Political Sciences Journal
Nation-Building in The Fragile States: Iraq After 2003 as a Model
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The nation-building process in fragile states is complex, often involving multifaceted challenges and opportunities. A pertinent example is Iraq post-2003, which serves as a model to study the intricacies of rebuilding a nation in the aftermath of conflict. During this period, we witnessed a significant international intervention aimed at establishing democratic governance, fostering economic development, and restoring social stability. Iraq’s nation-building journey showcases both successes and shortcomings. Establishing a representative government marked a step towards inclusivity and political participation, yet sectarian tensions persisted, hindering cohesive national identity. Economic initiatives aimed to harness Iraq's oil resou

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Publication Date
Tue Jun 30 2020
Journal Name
College Of Islamic Sciences
Novelist character in the Iraqi press criticism – Fadhil Thamir as a model))
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The novel has recently received great attention from readers and before them writers, due to the role it is playing, and this indicates an important rule, which is whenever there is art or creativity, there must be a criticism of its own, and this criticism is certainly no less important than its owner, so we find There are critics who have their distinguished literary position in following up the narrative development, and trying to describe the transformation of its elements, including Professor Fadel Thamer, and whoever wants to approach an element of the novel as an explorer, he must stand on the visions of this critic about it, and this is what made us take the element (personality) Tracking the most important opinions of the critic

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Publication Date
Thu Oct 18 2018
Journal Name
Al–bahith Al–a'alami
The Pressures Affecting the Performance of Iraqi Media before the Legislative Elections of 2018 (Iraqi Satellite News Channel- as a Model): A Survey Study  Dr.Safad Husam Hammody
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The modernity of election practices of the elections in Iraq, according to the democratic approach, has led to a struggle between political rival forces reflecting a deep pressure on the tools involved in the management, marketing or control of these elections across the general social level. Hence the problem of research resides in answering the following question: What is the nature and size of the pressures affecting the media performance of Al-Iraqia News channel before the legislative elections of 2018 in Iraq?
      The objectives of the research were the following:
1. to identify the nature of the pressures that limit the Al-Iraqia News channel’s perfo

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Publication Date
Tue Jul 01 2025
Journal Name
South African Journal Of Chemical Engineering
Expired azithromycin and cephalexin as corrosion inhibitors for aluminum in saline-acidic solution
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Publication Date
Mon Mar 15 2021
Journal Name
The Journal Of Legal And Social Sciences
The Limitations on the Judge’s Authority in Judicial Interpretation – France as a Model
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When exercising their authority in the jurisprudence, judges are subject to a set of restrictions that they must adhere to, as they do not want their jurisprudence to be accepted and welcomed by law practitioners in general, and legal scholars in particular, and in contrast to it, the arrows of criticism and defamation will extend to that jurisprudence, and then they will have to reverse them . Perhaps the most important of those restrictions imposed on judges is their observance of justice between the parties to the lawsuit through their lack of bias for one of the parties at the expense of the other, in addition to their observance of public order and public morals, as well as their observance of the legal texts that they work under its u

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Publication Date
Tue Apr 18 2023
Journal Name
Corporate Reputation Review
The Absorptive Capacity of Knowledge as an Approach for Building Strategic Reliability in the Sponge Organizations/Small Organizations in Kirkuk Governorate as a Model
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Publication Date
Mon Nov 10 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Photogrammetric analysis of facial soft tissue profile of Iraqi adults sample with Class II div.1 and Class III malocclusion: (A comparative study)
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Background: The purposes of this study were to determine the photogrammetric soft tissue facial profile measurements for Iraqi adults sample with class II div.1 and class III malocclusion using standardized photographic techniques and to verify the existence of possible gender differences. Materials & methods: Seventy five Iraqi adult subjects, 50 class II div.1 malocclusion (24 males and 26 females), 25 class III malocclusion (14 males and 11 females), with an age range from 18-25 years. Each individual was subjected to clinical examination and digital standardized right side photographic records were taken in the natural head position. The photographs were analyzed using AutoCAD program 2007 to measure the distances and angles used in t

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Publication Date
Fri Sep 15 2023
Journal Name
Bionatura
A comparison of VCAM-1 and ICAM-1 as atherosclerosis risk factors in patients with systemic lupus erythematosus from Iraq
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All major organs may be impacted by the connective disease systemic lupus erythematosus, a separate risk factor for coronary artery disease (CAD). Adhesion molecules like intercellular adhesion molecules (ICAM) and vascular cell adhesion molecules (VCAM) can detect endothelial damage and dysfunction, which appear to play a crucial role. This study investigated whether people with SLE had elevated subclinical and clinical atherosclerosis risk factors. Traditional CAD risk factors such as smoking, hypertension, and hyperlipidemia cannot entirely explain this elevation. It is thought that immunological dysfunction also increases CAD risk in SLE patients. The study aimed to assess early endothelial changes in SLE Iraqi female patients w

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Publication Date
Wed Aug 17 2022
Journal Name
Aip Conference Proceedings
The effect of using Gaussian, Kurtosis and LogCosh as kernels in ICA on the satellite classification accuracy
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This study focusses on the effect of using ICA transform on the classification accuracy of satellite images using the maximum likelihood classifier. The study area represents an agricultural area north of the capital Baghdad - Iraq, as it was captured by the Landsat 8 satellite on 12 January 2021, where the bands of the OLI sensor were used. A field visit was made to a variety of classes that represent the landcover of the study area and the geographical location of these classes was recorded. Gaussian, Kurtosis, and LogCosh kernels were used to perform the ICA transform of the OLI Landsat 8 image. Different training sets were made for each of the ICA and Landsat 8 images separately that used in the classification phase, and used to calcula

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