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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 Dec 06 2009
Journal Name
Baghdad Science Journal
Purification and Characterization of protease from Zahdi dates plam seeds (Phoenix dactylifera L.)
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Proteinases (E.C.3.4.21) family are widely distributed in the nature; it was present in animals tissues , plants and microbial cell . Protease was purified from Zahdi seed (Phoenix dactylifera L.) by several steps included ammonium sulphite ppt (75%) saturation and dialyzed against the 80mM sodium phosphate buffer at pH 7.5 . The enzyme specific activity was 407.62 unit/mg protein. The obtained extract was purified by DEAE-Cellulose column followed by gel filtration through Sephacyl S-200 column .The enzyme specific activity ,yield and purification fold were 1873.49 unit/mg protein, 22.99 and 58.42% respectively. The results of protease characterization showed that the molecular weight was 25118 daltons as determined by gel f

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Publication Date
Tue Jul 31 2018
Journal Name
Revue Académique De La Recherche Juridique
Jurisdiction in the contract of professional football player ((comparative study))
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Is no longer a football player looks to sport as a means of entertainment and physical development. But become see as part of The economic and is getting in return for the effort of، Through a contract with a club to organize the activity which is called a contract of professional, This contract is similar to the rest of the contracts in terms of problems and dispute that arise during the implementation or after it ends because of the nature of sports to such disputes and privacy being subject to special rules (regulations, national and international professional) required that subject to judicial bodies private mission confined settle sports disputes these entities and is affiliated unions legal committees and the court of arbitration for

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of International Oral Health
Endothelin-1 is a surrogate biomarker link severe periodontitis and endothelial dysfunction in hypertensive patients: The potential nexus
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Aim and Objectives: The objective of this study was to illustrate the link between periodontitis (PO) and endothelial dysfunction in hypertensive patients. Materials and Methods: This cross‑sectional study involved 53 hypertensive patients with or without PO compared with 28 healthy controls. On the basis of the study protocol, the participants were divided into three groups: Group (1): 24 patients with hypertension only, Group (2): 29 patients with hypertension and PO, and Group (3): 28 healthy controls. Lipid profile, endothelin‑1 (ET‑1), and high‑sensitivity C‑reactive protein (hs‑CRP) were measured. Blood pressure and body mass index (BMI) were evaluated. Diagnostic criteria of severe PO periodontal indices including plaque

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Publication Date
Sun Aug 28 2016
Journal Name
World Journal Of Pharmacy And Pharmaceutical Sciences
AN INSIGHT ON THE IDENTIFICATION OF CANCER STEM CELLS USING NOVEL IMMUNOLOGICAL AND MOLECULAR STRATEGIES
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Cancer stem cells (CSCs) are defined as a population of cells present in tumours, which can undergo self-renewal and differentiation. Identification and isolation of these CSCs using putative surface markers have been a priority of research in cancer. With this background we selected pancreatic normal and tumor cells for this study and passaged them into animal tissue culture medium. Further staining was done using alkaline phosphatase and heamatoxilin staining. Blue to purple colored zones in undifferentiated pluripotent stem cells and clear coloration in the chromatin material indicated pancreatic cells. Further studies on the cell surface marker CD 44 were done using ELISA. For this, the protein was extracted from cultivated normal and t

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Independent government agencies in Iraq / Integrity Commission a model
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The state did not witness the emergence of independent bodies because of the nature of the ruling regimes that were characterized by political tyranny represented by the king at the time, as is the case with Greece and the Greeks and Persia and the Romans and others. As for the Islamic state, which emerged later, it saw the emergence of what looks like independent bodies that we see today, There was the so-called Diwan Al-Hesba and the Ombudsman's Office as an independent body from the Islamic State, which operated independently to support the oppressed and the equitable distribution of financial resources, even though it was headed by well-known governors of justice and honesty. A state in the modern era, many countries, especially in E

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Production of fibrinolytic protease from various fungal isolates and species 2.Determination of optimum conditions for enzyme production from Pleurotus ostreatus
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The optimum conditions for production of fibrinolytic protease from an edible mushroom Pleurotus ostreatus grown on the solid medium , Sus medium, composed of Sus wastes (produced from extracted medicinal plant Glycyrrhiza glabra) were determined. Addition of 5% of Soya bean seeds meal in Sus medium recorded a maximum fibrinolytic protease activity resulting in 7.7 units / ml. The optimum moisture content of Sus medium supplemented with 5% Soya bean seeds meal was 60% resulting in 7.2 units / ml.Pleurotus ostreatus produced a maximum fibrinolytic protease activity when the spawn rate,pH of medium and incubation temperature were 2,6 and 30°C, respectively. The maximum fibrinolytic protease activity was 7.6 units / ml when incubat

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Publication Date
Sun Jan 30 2022
Journal Name
Gsc Biological And Pharmaceutical Sciences
Comparative anatomical study for fruits of some species of Bunium L. (Umbelliferae) in Iraq
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Bunium is one of the interested genus that grow in different region of Iraq, it is within the family Umbelliferae (Apiaceae), and the species within this family have a considerable fruit characteristics. The species that were chosen in this study are: B. brachyactis (Post) H. Wolff, B. caroides (Boiss.) Hausskn. Ex Bornm., B. chaerophylloides (Regel& Schmalh.) Drude, B. rectangulum Boiss. & Hausskn., B. verruculosum C.C.Towns. and B. avromanum (Boiss.& Hausskn) Drude., the study found that the fruits of these species have 5 protrusions different in size but all have the same number of vittae, but some are semiler in size and some are not, the number of vascular element are varied between these species, anatomical charact

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Publication Date
Sun Jun 07 2009
Journal Name
Baghdad Science Journal
Use of Nicotiana tobaccum extractions as a molluscicide to the snail of Bulinus truncates
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Nicotiana tobaccum L (Solanacea) extracts are used as a mollusciede to the snail Bulinus truncatus the intermediate host of urinary Schistosomiasis. LC50 of the extracts to the snail with 24 hour was 3.27 ml/l? 48 hour was 3.33 ml/l? 72 hour was 2.67 ml/l and 96 hour was 2.28ml/l. This study showed the ability to use the leaf extracts in the control of this type of snail.

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Publication Date
Thu Jan 01 2009
Journal Name
Iraqi Journal Of Science, Supplement 0f 2009
THE RELATIVE QUANTUM EFFICIENCY OF ANTHRACENE SOLUTION AS A FUNCTION OF LIGHT EXPOSURE DURATION
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Abstract In this paper the effect of light exposure duration on Anthracene solution in chloroform is studied. It is found that: the Anthracene solution change its color when it is exposed to light, and that its relative quantum efficiency, Φ, decreases as the light exposure duration, t, increases and this govern by following empirical equation:- Φ = 0.7918-0.0762 In (t)

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
HISTORY AND MODERNITY OF POETRY AS : A Reference Of The Modern Poem In Iraq
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One of the most important intellectual issues, which receive attention is the issue of modernity, it has occupied the scholars of all time. However, modern poetry used to have special care in Iraq and in the Arab countries .. it is not strange that the concept of modernity is linked to history .. or having history as the most important dimension of its dimensions .. because Arab poetry is historical and it is moving into an area of ​​the past that is still active in terms of language and literary image .. When some poets found that changing and modernizing poetry became a necessity of evolution, and one of the fundamentals of modernization, the cultural impact did not respond to the desire of poets, and their impulse in modern poetry

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