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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 Jul 01 2025
Journal Name
Kirkuk Journal Of Medical Sciences
Socio-Demographic Characteristics of Individuals Seeking Non-Surgical Aesthetic Procedures: A Cross-Sectional Study
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
A Kinetic Study on Microwave- assisted Extraction of Bioactive Compounds from Rosmarinus Officinalis L
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Due to the importance of the extraction process in many engineering and medical industries, in addition to great interest in medicinal plants, in this research, microwave-assisted extraction has been applied to extract some active compounds from Rosmarinus officinalis leaves.  The optimal extraction conditions were then determined by calculating the ratio and extraction efficiency. The process has also been described through kinetic study by applying five  kinetic models, the Hyperbolic diffusion model,  Power low model, the First order reaction  model, Elovich's model, and Fick's second law diffusion model and determining their compatibility with the studies operation, and determining the kinetic constants for each model. The result

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Publication Date
Sun Jul 01 2018
Journal Name
Vacuum
Stability, electronic and vibrational properties of GaAlN wurtzoid molecules and nanocrystals: A DFT study
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Publication Date
Sat Jan 01 2011
Journal Name
Iraqi Postgraduate Med J
Effects of herbs–containing phytoestrogens on rat testis: A histological, histochemical and biochemical study
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ABSTRACT: BACKGROUND: Estrogens has traditionally been known as the female hormone, but this idea has been challenged in early 1990’s and an essential physiological role for estrogen in male fertility was identified. Phytoestrogens are naturally occurring non-steroidal plant chemicals that can act like the female hormone estrogen. The herbs ( anise alfalfa and vervain ) chosen in this study contain phytoestrogens. OBJECTIVE: Previous studies demonstrated controversy of the effects of phytoestrogens on the rat testes .Hence, the present investigation was undertaken to investigate the influence of typical dose of herbs containing phytoestrogen on the rat testis. MATERIALS AND METHODS: Twenty-four apparently normal mature male rats we

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Publication Date
Wed May 01 2019
Journal Name
Heliyon
Toward liveable commercial streets: A case study of Al-Karada inner street in Baghdad
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Publication Date
Mon Jun 30 2008
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Kinetic Study on Catalytic Wet Air Oxidation of Phenol in a Trickle Bed Reactor
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Kinetics study on the phenol oxidation by catalytic wet air oxidation (CWAO) using CuO.NiO/Al2O3 as heterogeneous catalyst is presented. 4 g/l phenol solution of pH 7.3 was oxidized in a trickle bed reactor with gas flow rate of 80% stochiometric excess (S.E).. In order to verify the proposed kinetics, a series of CWAO experimental tests were done at two temperatures (140 and 160° C), oxygen partial pressures (9 and 12 bar), and weight hourly space velocity (WHSV) (1, 1.5, 2, 2.5, and 3 h-1). According to Power Law, the reaction orders are found to be approximately 1 and 0.5 with respect to phenol concentration and oxygen solubility, respectively. These values favorably compare with those cited in the literature for intrinsic kinetics,

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Publication Date
Sun Mar 01 2026
Journal Name
Al–bahith Al–a'alami
DICTION (IN ARAB SATELLITE CHANNELS) A SIGNAL SYSTEM : (study of written And oral patterns)
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Communication has seen a big advancement through ages; concepts, procedures and technologies, it has also seen a similar advancement of language. What unites language and media is the fact that each one of them guides and contributes to the other; media exists and results from language and from the other sign systems, and what strengthens this connection is the symbolic language system, as media helps it by providing knowledge and information. The change that occurred through time must leave a significant trace in the media, for example Diction, which has changed concerning development and growth, also the ways and mediums of media have become manifold and widespread. This change affected the recipient whether it was a reader, listener o

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Publication Date
Tue Oct 01 2019
Journal Name
Safety Science
Perceived management commitment and psychological empowerment: A study of intensive care unit nurses’ safety
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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
Prothrombin Time role in Head Injury & Intracranial Hematomas, A prospective Study of 325 cases
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Objective: Aimed to asses the role of PT estimation in early diagnosis and predicting the extent and the outcome of head injury with ICerH and/ or Contusion
Method :PT was measured by Digiclot 818
Group –1: One hundred consecutive head injured patients admitted at Neurosurgical and Al Ramadi teaching hospitals were initially estimated for prothrombin time and subsequently scanned
Group-2 : Two hundred twenty five consecutive non scanned head injured patients admitted to Neurosurgical and Al Ramadi teaching hospitals were estimated with prothrombin time at the time of insult and subsequently for the next two weeks Al – Kindy Col Med J 2012; Vol. 8 No. 1 P: 54
Clinical and neurological evaluation (GCS) score in addition to

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Article Structural violence: A study In Johann Galtung's theory of explanation he violence t
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This study deals with the subject of violence, but from another perspective, it has not been emphasized in contemporary studies of violence in Arabic and raqi universities, which is the structural or institutional aspect of violence. Traditional studies have focused their analysis of violence on the direct side the violence, The other side of the violence is the hidden violence, which is characterized by a lack of clarity of the underlying factors and its effects are not arises, which makes it the most serious violence, which requires a deep research into the social, political, economic, cultural and psychological structure of society (individuals and institutions). This study was based on the theory of the Norwegian scientist (J

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