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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
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Cephalothin as a Carrier of 6-Mercaptopurine for Targeting Cancer Tissues
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A lower extracellular pH is one of the few well-documented physiological differences between tumour and normal tissues. On the other hand, elevated glutathione (GSH) level has been detected in many tumours compared with healthy surrounding tissues. The compound II: 3-(9H-purin-6-yl-thio) carbonothionyl methyl-8-oxo-7-(2-thiophen-2-yl) acetamido-5-thia-1-azabicyclo-4-octo-ene-carboxylic acid was a cephalothin derivative contain 6-mercaptopurine (6-MP). Compound II react with general base catalysis in slightly acidic pH or with sulfhydryl nucleophiles to release the chemotherapeutic drug 6-MP. The generation of compound II was accomplished following multistep reaction procedures. The structure of compound II and its intermediate was confir

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Publication Date
Sun Dec 31 2023
Journal Name
Iraqi Geological Journal
A Comparative Reservoir Study of Zubair and Nahr Umr Formations in Subba Oilfield, Southern Iraq
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The lower Cretaceous sandstones of Zubair and Nahr Umr formations are the main producing reservoirs in Subba oilfield in southern Iraq. Key differences in their petrophysical and depositional attributes exist affecting their reservoir characteristics. The evaluation of well logs and core porosity-permeability data show better reservoir properties in Nahr Formation. The Litho-saturation logs indicate greater thickness of oil-saturated reservoir units for Nahr Unr Formation associated with lower values of shale volume, and higher values of effective porosity. In addition, higher values of permeability for Nahr Umr Formation is suggested by applying porosity-irreducible water saturation cross plot. The reducing reservoir quality of Zub

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Publication Date
Thu Jan 30 2014
Journal Name
Al-kindy College Medical Journal
A Comparative Study on Treatment of Diabetic Foot Infection by Acetic Acid, Rifocin and Probiotics
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Introduction: Diabetic foot infections are one of the most severe complications of diabetes. This study was aimed to determine the common bacterial isolates of diabetic foot infections and the in vitro antibiotic susceptibility then treatment.
Methods: A swab was taken from the foot ulcer, and the aerobic bacteria were isolated and identified by cultural, microscopic and biochemical test, then by api-20E system. After that their antibiotic susceptibility pattern was determined. Then local and systemic treatment was used to treat the diabetic foot patients.
Results: Bacterial isolates belonging to twelve species were obtained from diabetic foot patients. Gram (-) bacteria were the predominant pathogens in the diabetic foot infection

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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Design and Comparative Study of a one and Two Stage Blumlein Circuit TEA Nitrogen Laser
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Two Prototypes of Transversely Excited at atmospheric pressure (TEA) Nitrogen laser systems (One Stage Blumlein Circuit and Two Stage Blumlein Circuit) were fabricated and operated. High voltage power supply with variable operating voltage (0-20 kv) and operating current (1-3A) was built and tested successfully. The gas flow rate of 15 L/ min and 10 L/ min for OSBC and TSBC was used. The performance of the fabricated systems was studied extensively reaching to the optimum operating conditions. The obtained laser output energy for the first system has linear relationship with the applied voltage. The maximum output energy was about (1.14 mJ) with (10.40) ns pulse duration and the half-wave divergence angle was about (0.1455 m rad). In the

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Publication Date
Sat Oct 01 2022
Journal Name
Journal Of Pakistan Association Of Dermatologists
Zinc as an essential element for normal immune reactions and as a therapeutic agent for autoimmune diseases
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Publication Date
Sat Dec 30 2023
Journal Name
مجلة الذكوات البيض
Assessing Accuracy and Interaction in a Speaking Test : AN Analytical study. تقييم الدقة و التفاعل في اختبار المحادثة: دراسة تحليلية
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This paper deals with one of the most important issues in a foreign language teaching and learning, i.e. speaking test assessment. After giving a survey of literature written on the meaning and definition of a speaking test assessment, two sections have been devoted to tackle the most important issues in this topic. Section one, which is the theoretical part of this paper, sheds light on the basic definitions of the term ‘speaking assessment’ which are, according to the researcher’s point of view, sufficient to cover the area of the study. This section based on applied linguistic theories and researches in order to enhance our understanding of the what is meant by «a speaking test assessment«In addition,it explains the most importan

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Publication Date
Thu Aug 31 2017
Journal Name
Journal Of Engineering
Reactive Adsorption Desulfurization by Nanocrystalline ZnO/Zeolite A Molecular Sieves
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      Nanocrystalline ZnO/Zeolite type A composite was prepared by simple method of operation by . the precipitation of zinc oxide and loading on zeolite 5A in one step. Characterization was made by X-ray diffraction (XRD), X-ray fluorescence(XRF), N2  adsorption- desorption for BET surface area, and Atomic force microscopy (AFM). Results showed that zinc oxide was loaded on zeolite as noticed by the characteristic peaks and was of nano scale having an average diameter of 88.57nm. The percentage loading of ZnO on zeolite A was 28.37% and the surface area was 222m2/g. The activity of the prepared catalyst was examined in the desulfurization of double hydrogenated diesel fuel. The process was investigated in a

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Publication Date
Fri Jan 01 2021
Journal Name
Materials Today: Proceedings
Synthesis of gamma biguanides butyric acid analogues as HDAC inhibitors and studying their cytotoxic activity
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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of The College Of Languages (jcl)
Linguistic contast between bilateral and trilateral roots in Semitics languages (Arabic and Syriac as a model)
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The present study investigates the relation between the biliteral and triliteral roots which is the introduction to comprehend the nature of the Semitic roots during its early stage of development being unconfirmed to a single pattern. The present research is not meant to decide on the question of the biliteral roots in the Semitic languages, rather it is meant to confirm the predominance of the triliteral roots on these languages which refers, partially, to analogy adopted by the majority of linguists. This tendency is frequently seen in the languages which incline to over generalize the triliteral phenomenon, i. e., to transfer the biliteral roots to the triliteral room, that is, to subject it to the predominant pattern regarding the r

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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