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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
Mon Apr 17 2017
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
10.28936 STUDY OF THE KINETIC AND ADSORPTION ISOTHERM PARAMETERS FOR REMOVING COPPER AND IRON IONS FROM AQUEOUS SOLUTIONS BY USING AGRICALTURAL BY-PRODUCTS.: STUDY OF THE KINETIC AND ADSORPTION ISOTHERM PARAMETERS FOR REMOVING COPPER AND IRON IONS FROM AQUEOUS SOLUTIONS BY USING AGRICALTURAL BY-PRODUCTS.
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Wheat straw was modified with malonic acid in order to get low cost adsorbent have a good ability to remove copper and ferric ions from aqueous solutions, chemical modification temperature was 120°C and the time was 12 h. Parameters that affect the adsorption experiments were studied and found the optimum pH were 6 and 5 for copper and iron respectively and the time interval was 120 min and the adsorbent mass was 0.1 g. The values for adsorption isotherms parameters were determined according to Langmuir [qmax were 54.64 and 61.7 mg/g while b values were 0.234 and 0.22 mg/l] , Freundlich [Kf were 16.07 and 18.89 mg/g and n were 2.77 and 3.16], Temkin [B were 0.063 and 0.074 j/mol and At were 0.143 and 1.658 l/g] and for Dubinin-Radushkev

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Publication Date
Thu Dec 30 2021
Journal Name
Diyala Agricultural Sciences Journal
A Study of Some Biological Aspects of Pacu Piaractus Brachypomus (G. Cuvier, 1818)
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The present study attempts to shed light on some biological aspects and characteristics of Piaractus brachypomus, including some biometrics, phenotypic and feeding pattern that characterizes this species. Besides, the study touches upon the body shape and the Otolith. These fish species have recently been seen frozen in the Iraqi local market. The standard length of fish specimens in this study reach 26.55cm it exceeded the specimens of Pacu fish collected from other studies from other countries, As well the specimens weight was 632gm it exceeded other studies mentioned in this manuscript. As the irregularity in the distribution of teeth rows, especially in the lower jaw was clear in our specimens. The average weight of some skull b

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Petroleum Research And Studies
A Numerical Study of Tertiary Oil Recovery by Injection of Low-Salinity Water
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The injection of Low Salinity Water (LSWI) as an Enhanced Oil Recovery (EOR) method has recently attracted a lot of attention. Extensive research has been conducted to investigate and identify the positive effects of LSWI on oil recovery. In order to demonstrate the impact of introducing low salinity water into a reservoir, simulations on the ECLIPSE 100 simulator are being done in this work. To simulate an actual reservoir, an easy static model was made. In order to replicate the effects of injecting low salinity water and normal salinity, or seawater, the reservoir is three-phase with oil, gas, and water. It has one injector and one producer. Five cases were suggested to investigate the effect of low salinity water injection with differen

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Publication Date
Tue May 31 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities
A Critical Discourse Analysis Study of Silence in Selected Texts of Virginia Woolf
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BN Rashid, Social Sciences, 2022

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Publication Date
Thu Mar 10 2022
Journal Name
Alustath Journal For Human And Social Sciences
Cognition Construction of First Language of Translator ‎Education in Iraq: A Correlation Study
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The majority of Iraqi translator-student have problems at two main levels: the conceptual level and the productive level. From different perspectives, such problems are either related to ‘language’ or to ‘cognition’. This binary view is an indication to the implicit and interchangeable relationship between language and cognition. The relationship between cognition language and translator starts with the first language and its effect on the Iraqi translators. Identifying the effect is the aim of the present study. It is hypothesized that Iraqi students are negatively influenced by the problems and weaknesses of first language schema. This reflects the major claim and later concludes that first language instruction in the Iraq

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Publication Date
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Determination of optimal conditions for laccase production by Pleurotus ostreatus using sawdust as solid medium and its use in phenol degradation
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The ability of four local fungal isolates for extracellular laccase production has been tested with five grams 1:1(w/v) humidified sawdust as substrate in mineral salt medium. After 21 day of incubation at 25±1 ? C and using one mycelial plug (5mm), higher level of laccase activity (0.15U/ml) and specific activity (15U/mg) were observed by Pleurotus ostreatus in comparison with other fungal isolates. The results of optimum conditions for laccase production from selected isolate showed that, the maximum laccase activity (0.55U/ml) and specific activity (55U/mg) were obtained at moisture ratio 1:3 (w/v), using 3 mycelial plugs (5 mm), after 15 days incubation period at 25±1 ? C. The results of phenol degradation by crud laccase revealed th

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Publication Date
Wed Jan 01 2014
Journal Name
Department Of Bioengineering And Sciences
1 T.R. KAHRAMANMARAŞ SÜTÇÜ İMAM UNIVERSITY GRADUATE SCHOOL OF NATURAL AND APPLIED SCIENCE Cloning and overexpression of Lactobacillus acidophilus bile salt hydrolase A gene (bshA) in Escherichia coli
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The bile salt hydrolase gene (bshA), encoding bile salt hydrolase enzyme (EC 3.5.1.24) from probiotic isolate Lactobacillus acidophilus Ar strain which is responsible for assimilation cholesterol were studied in the present work. About 801 bp in length DNA fragment of Lb. acidophilus Ar strain was amplified by PCR techniques. Two restriction sites (PstI/SacI) were added to each end of that fragment for manipulation of DNA during cloning. Amplified fragment inserted into pJET1.2\blunt end vector and pMG36e vector respectively. pJET1.2\blunt end vector is overexpression plasmid for E. coli MC1022, and pMG36e vector is a shuttle vector which is able to replicate in both E. coli and lactic acid bacteria. The resulted constructs were named as pJ

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Publication Date
Wed Jun 19 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Impact of the Knowledge Economy in the Tax Examination Survey: Study of A Simple of Auditors Views in the General Commission of Tax
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   The organizations and institutions of the developed countries have given attention to the subject of the knowledge economy by using advanced technology in the function of tax examination because of the important and effective role in ensuring the accuracy of the tax accounting process procedures, But the General Commission of taxes is still using traditional methods in the field of  tax examination which affects the performance of its work. This research aims to explain the level of effect on introducing advanced methods of Economics and knowledge represented by advanced communication technology in the field of practicing tax examination function in the General Commission of taxes, A questionnaire has been used as a mea

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Publication Date
Fri Jun 30 2023
Journal Name
International Journal Of Intelligent Engineering And Systems
DeepFake Detection Improvement for Images Based on a Proposed Method for Local Binary Pattern of the Multiple-Channel Color Space
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DeepFake is a concern for celebrities and everyone because it is simple to create. DeepFake images, especially high-quality ones, are difficult to detect using people, local descriptors, and current approaches. On the other hand, video manipulation detection is more accessible than an image, which many state-of-the-art systems offer. Moreover, the detection of video manipulation depends entirely on its detection through images. Many worked on DeepFake detection in images, but they had complex mathematical calculations in preprocessing steps, and many limitations, including that the face must be in front, the eyes have to be open, and the mouth should be open with the appearance of teeth, etc. Also, the accuracy of their counterfeit detectio

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Publication Date
Sun Jan 01 2023
Journal Name
Materials Today: Proceedings
Preparation, characterization and preliminary cytotoxic evaluation of 6-mercaptopurine-coated biotinylated carbon dots nanoparticles as a drug delivery system
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