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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
Political Sciences Journal
The economic dimensions of the railway link between Iraq and Kuwait and the role of national alternatives (Faw port and the dry canal as a model(
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   Decision-makers in each country work to define a list of internal and external interests, goals and threats to their countries according to the nature of their awareness of these interests, goals and threats. 

  Hence, Iraq is not an exception to this rule, and the process of evaluating its interests and the objectives of its foreign policy is subject to the pattern of awareness of decision-makers and the influencing forces in defining its basic interests, which often witness some kind of difference in defining them, evaluating their importance and determining the size of the threats they face. And among these interests and threats that have witnessed a difference in the assessment of their

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Publication Date
Sun Jan 02 2022
Journal Name
Neuroquantology
Treatment of primary trigeminal neuralgia: A comparative study of microvascular decompression surgery and stereotactic gamma knife radiosurgery
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Objectives To compare the clinical efficacy of microvascular decompression surgery (MVD) and gamma knife radiosurgery (GKR) as a treatment for patients with primary trigeminal neuralgia (TN) and evaluate the outcome regarding pain relief, recurrence, and complications with both modalities of treatment. Patients and Methods A randomized prospective study conducted in SaadAlwitry Neurosciences Hospital, Baghdad, Iraq. Eighty-four patients with TN from January 2016 to January 2018, 45 patients had GKR while 39 patients treated with MVD. The pain evaluated pre-and post-operatively using the Barrow Neurological Institute Pain Intensity scale (BNIPI), visual analog scale (VAS) and Brief Pain Inventory Facial (BPI-Facial) scoring systems. In GKR p

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Publication Date
Thu Dec 01 2022
Journal Name
Bulletin Of Electrical Engineering And Informatics
A model for incorporating suitable methods of usability evaluation into agile software development
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The challenge to incorporate usability evaluation values and practices into agile development process is not only persisting but also systemic. Notable contributions of researchers have attempted to isolate and close the gaps between both fields, with the aim of developing usable software. Due to the current absence of a reference model that specifies where and how usability activities need to be considered in the agile development process. This paper proposes a model for identifying appropriate usability evaluation methods alongside the agile development process. By using this model, the development team can apply usability evaluations at the right time at the right place to get the necessary feedback from the end-user. Verificatio

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Publication Date
Thu Jun 27 2024
Journal Name
Malaysian Journal Of Mathematical Sciences
Dynamics of a Social Model for Marriage and Divorce Relationship with Fear Effect
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The objective of this article is to delve into the intricate dynamics of marriage relationships, exploring the impact of emotions such as fear, love, financial considerations and likability. In our investigation, we adopt a perspective that acknowledges the nonlinear nature of interactions among individuals. Diverging from certain prior studies, we propose that the fear element within the context of marriage is not a singular, isolated factor but rather a manifestation resulting from the amalgamation of numerous social issues. This, in turn, contributes to the emergence of strained and unsuccessful relationships. Unlike conventional approaches, we extensively examine the conditions essential for the existence of all socially signifi

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Publication Date
Sun Dec 01 2002
Journal Name
Iraqi Journal Of Physics
A Hyperbolic Potential Field Model for Designing an Einzel Lens of Low Aberrations
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An analytical model in the form of a hyperbolic function has been suggested for the axial potential distribution of an electrostatic einzel lens. With the aid of this hyperbolic model the relative optical parameters have been computed and investigated in detail as a function of the electrodes voltage ratio for various trajectories of an accelerated charged-particles beam. The electrodes voltage ratio covered a wide range where the lens may be operated at accelerating and decelerating modes. The results have shown that the proposed hyperbolic field has the advantages of producing low aberrations under various magnification conditions and operational modes. The electrodes profile and their three-dimensional diagram have been determined whi

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Publication Date
Thu Oct 01 2009
Journal Name
Jssdds
Topical 10% lactic acid solution in the treatment of pityriasis versicolor in comparison with topical 1% clotrimazol solution (single-blind, comparative and therapeutic study)
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KE Sharquie, AA Noaimi, AM Oweid, JSSDDS, 2009 - Cited by 2

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Publication Date
Fri Oct 23 2020
Journal Name
Biomed Research International
A Computational Model of the Brain Cortex and Its Synchronization
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Obtaining the computational models for the functioning of the brain gives us a chance to understand the brain functionality thoroughly. This would help the development of better treatments for neurological illnesses and disorders. We created a cortical model using Python language using the Brian simulator. The Brian simulator is specialized in simulating the neuronal connections and synaptic interconnections. The dynamic connection model has multiple parameters in order to ensure an accurate simulation (Bowman, 2016). We concentrated on the connection weights and studied their effect on the interactivity and connectivity of the cortical neurons in the same cortical layer and across multiple layers. As synchronization helps us to mea

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Formulating a strategy for the Northern Oil Company(Case Study)
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                  The research aims to present a proposed strategy for the North Oil Company, and the proposed strategy took into account the surrounding environmental conditions and adopted in its formulation on the basis and scientific steps that are comprehensive and realistic, as it covered the main activities of the company (production and exploration activities, refining and refining activities, export and transport of oil, research and development activity, financial activity, information technology, human resources) and the (David) model has been adopted in the environmental analysis of the factors that have been diagnosed according to a

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Publication Date
Sun Nov 16 2025
Journal Name
Journal Of Economics And Administrative Sciences
Formulating a strategy for the Northern Oil Company(Case Study)
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يهدف البحث الى تقديم استراتيجية مقترحة لشركة نفط الشمال ، وأخذت الاستراتيجية المقترحة بنظر الاعتبار الظروف البيئية المحيطة واعتمدت في صياغتها على اسس وخطوات علمية تتسم بالشمولية والواقعية ، اذ انها غطت الانشطة الرئيسية في الشركة (نشاط الانتاج والاستكشاف , نشاط التكرير والتصفية , التصدير ونقل النفط , نشاط البحث والتطوير , النشاط المالي , تقنية المعلومات , الموارد البشرية ) وقد اعتمد نموذج (David) في التحليل البيئي

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Publication Date
Sat May 08 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Sequencing of IL-10 Gene Promoter for -592 (A/C) and -1082 (A/G) Positions in Iraqi Children Patients with Type 1 Diabetes Mellitus
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We studied the relationship between DNA sequencing of interleukin-10 (IL-10) gene promoter for -1082 (A/G) and -592 (A/C) positions with the concentration of IL-10 in blood serum of Iraqi children with type 1 diabetes mellitus (T1D). Fifty blood serum samples collected from children with age ranged between 7-12 years. Thirty-five blood samples collected from patient children with T1D, and compared with 15 healthy children age matched as control sample. The results revealed decreasing in anti-inflammatory IL-10 concentration in T1D patient’s blood serum (0.068 Pg/ml) as compared with the control sample (0.111 Pg/ml). No significant differences were found in interleukin concentration between the studied samples when they analyzed with the M

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