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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 Jun 01 2014
Journal Name
Baghdad Science Journal
Biological activity and protease inhibitor from watery extract of lentil (Lens culinaris) against some bacterial species
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Biological activity substances was investigated in watery extract of lentil which found to contain phenols, tannin, saponins and resins while, flavons, terpens and steroids were not exist in the extract details explained that 5%, 10% of lentil extract largly inhibited the growth of Psedumonas aeruginosa then Escherichia coli and Bacillus subtilis. The growth of both Staphylococcus aureus and Salmonella typhimurium were slightly affected by all extract concentration. Extracellular protease were screened in all bacterial species under study. Complete inhibition was achieved for extracellular protease while different percentage of protease inhibition were seen for intracellular proteases.

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Publication Date
Sun Jan 01 2023
Journal Name
Rawal Medical Journal
Efficacy of lumbar interlaminar epidural steroid injections for lumbar spinal stenosis: A prospective study
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Objective: To study the effect of epidural spinal injection over one year in case of spinal stenosis. Methodology: This prospective study included 566 patients with spinal stenosis seen at Al-Kindy Teaching and Al-Sader, Hospitals who were treated by local epidural steroid injection. They were followed up for at least five subsequent visits after seven days, one month, three months, six months, and one year to assess efficacy. Result: Mean age of patients was 49.5 years, with a predominance of females (65%). L4/L5 was the most involved level in the spinal stenosis (70%). Grade II stenosis accounted for (45.4%) of cases. The pairwise comparison revealed that there was significant decrease in proportions of patients with pain in day

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Publication Date
Sat Mar 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Estimation of rock strength from sonic log for Buzurgan oil field: A Comparison study
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It is very difficult to obtain the value of a rock strength along the wellbore.  The value of Rock strength utilizing to perform different analysis, for example, preventing failure of the wellbore, deciding a completion design and, control the production of sand.  In this study, utilizing sonic log data from (Bu-50) and (BU-47) wells at Buzurgan oil field.  Five formations have been studied (Mishrif, Sadia, Middle lower Kirkuk, Upper Kirkuk, and Jaddala) Firstly, calculated unconfined compressive strength (UCS) for each formation, using a sonic log method.  Then, the derived confined compressive rock strengthens from (UCS) by entering the effect of bore and hydrostatic pressure for each formation.  Evaluations th

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Publication Date
Sun Dec 03 2017
Journal Name
Al-khwarizmi Engineering Journal
A theoretical study for increasing production of electric power from Iraqi steam power plants.
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This article conclude a theoretical study for the possibility to produce additional electric power from Iraqi steam power plants by  cutting – off high-pressure feed water heaters .  Three separated steam power plants which Dura , south –Baghdad and Nasria were studied . The investigation showed the possibity of increasing the electric power from 10 to 15% for Dura and Nasria , whereas 6% for south – Baghdad . According to the nowadays of operation to Iraqi steam power plants , the results showed that by cutting–off high  pressure feed water heaters we can generate additional electric power about 250 MW during 3-4 hrs. daily. In addition, the fuel consumption can be reduced in comparison with diesel generat

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Publication Date
Thu Jun 20 2019
Journal Name
Baghdad Science Journal
Teen-Computer Interaction: Building a Conceptual Model with Thoughts- Emotion-Behaviour
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Teen-Computer Interaction (TeenCI) stands in an infant phase and emerging in positive path. Compared to Human-Computer Interaction (generally dedicated to adult) and Child-Computer Interaction, TeenCI gets less interest in terms of research efforts and publications. This has revealed extensive prospects for researchers to explore and contribute in the region of computer design and evaluation for teen, in specific. As a subclass of HCI and a complementary for CCI, TeenCI that tolerates teen group, should be taken significant concern in the sense of its context, nature, development, characteristics and architecture. This paper tends to discover teen’s emotion contribution as the first attempt towards building a conceptual model for TeenC

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Publication Date
Thu Jan 01 2015
Journal Name
Journal Of Toxicology
Acute β - N -Methylamino-L-alanine Toxicity in a Mouse Model
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The cyanobacterial neurotoxinβ-N-methylamino-L-alanine (BMAA) is considered to be an “excitotoxin,” and its suggested mechanism of action is killing neurons. Long-term exposure to L-BMAA is believed to lead to neurodegenerative diseases including Parkinson’s and Alzheimer’s diseases and amyotrophic lateral sclerosis (Lou Gehrig’s disease). Objectives of this study were to determine the presumptive median lethal dose (LD50), the Lowest-Observed-Adverse-Effect Level (LOAEL), and histopathologic lesions caused by the naturally occurring BMAA isomer, L-BMAA, in mice. Seventy NIH Swiss Outbred mice (35 male and 35 female) were used. Treatment group mice

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Use A State Space Model and Forecast House Prices in Baghdad.
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The purchase of a home and access to housing is one of the most important requirements for the life of the individual and the stability of living and the development of the prices of houses in general and in Baghdad in particular affected by several factors, including the basic area of the house, the age of the house, the neighborhood in which the housing is available and the basic services, Where the statistical model SSM model was used to model house prices over a period of time from 2000 to 2018 and forecast until 2025 The research is concerned with enhancing the importance of this model and describing it as a standard and important compared to the models used in the analysis of time series after obtaining the

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Publication Date
Sun Jan 01 2023
Journal Name
International Conference On Scientific Research & Innovation (icsri 2022)
Saccharomyces Cerevisiae as a human pathogen in renal transplant recipients
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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
Methionine as a Spacer between Poly Acrylic acid and Ampicillin
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In this work a novel drug delivery system through modification of poly acrylic acid with Methionine as a spacer between the poly acrylic acid which was converted to its acyl chloride and reacted with Methionine as spacer unit which has been reacted with Ampicillin drug. In vitro drug release study had been conducted successfully in basic medium in pH 7.4 and acidic medium in pH 1.1 at 37?. Due to many problems associated with drug release and, this modification could decrease the side effect of drug. The prepared prodrug polymer was characterized by spectra method [FTIR and 1H?NMR]. Physical properties and intrinsic viscosity of drug polymer were determined. The good results were obtained in the presence of spacer unit with compar

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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
political culture as a tool to analyse Decentralization Experience in
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It sheds light on the cultural dimension in the decentralized administration experience in Iraq as evaluation tool by adding a new dimension in studying decentralization in addition to the administrative, political and legal dimensions .The proposal of study is that without the civil political culture ,the administrative decentralization in Iraq which remains weak and it may be imposed to a set of problems. - The study includes an introduction, conclusion and a set of political and cultural issues , its components and it may have the political analysis of this culture and its role in determining the movement of the administrative decentralized movement in Iraq post 2003.

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