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bijps-1604
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 Jan 01 2018
Journal Name
Pakistan Journal Of Medical & Health Sciences
Prevalence of Peripheral Arterial Disease in End Stage Renal Disease Patients Undergoing Hemodialysis: A Cross-Sectional Study
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The chronic renal disease is a principle common medical dilemma in Iraq. Peripheral arterial disease (PAD) is a prevalent infirmity in the hemodialysis people. The aim of present study was to estimate the prevalence of PAD in subjects with end-stage renal disease (ESRD). This cross-sectional study was done between January 2016 and May 2017 on ESRD subjects regularly attending renal dialysis unit in Al-Kindy teaching hospital in Baghdad, Iraq. PAD was diagnosed on the base of the ankle-brachial index (ABI) measured by using a hand-held Doppler ultrasound. Subjects with ABI ≤0.9 were supposed positive for PAD. A total of 150 ESRD cases were analyzed. The mean age of the subject was 49.52±15 years. Majority of them were males 87(58%). Most

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Publication Date
Mon Jan 01 2024
Journal Name
WiadomoĊ›ci Lekarskie
Evaluation of clinical and demographical finding in patients with oral lichen planus: A retrospective cross sectional study
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Aim: To learn more about Oral Lichen Planus Iraqi patients, including their background information, symptoms, and prognosis. Materials and Methods: From the Oral and Maxillofacial Pathology Department, College of Dentistry, Baghdad University, we retrospectively reviewed the medical records of 68 patients with a histologically confirmed clinical diagnosis of oral lichen planus and subsequently contacted the patients by phone to evaluate their prognosis. Results: Females were more likely than males to experience severe pain; the reticular form of Oral Lichen Planus was the most prevalent at 38.2%, but the erosive type was more prevalent among females. Only 53 of 68 patients responded to phone calls. More than 37% of those respondents reporte

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
A Study of Epiphytic and Epipelic Algae in Al-Dora Site/Tigris River in Bagdad Province- Iraq
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There is a scarcity of data regarding algal flora of Tigris River in the territory of Baghdad. The present study deals with Tigris River in Al-Dora site in Baghdad province from November 2014 to June 2015 in order to shed light on its epiphytic Algae on (Phragmites australis) and epipelic algae. An amount of 183 and 154 species of epiphytic and epipelic algae are identified respectfully. The Bacillariophyceae (diatoms) are the dominant algal group followed by Cyanophyceae and Chlorophyceae. Moreover, 90 species are shared between two groups of algae (epiphytic and epipelic) and identified at the study site. Additionally, the seasonal variations and diversity of algal species are noticed. The highest number of epiphytic algae is 772.05 x 104

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Publication Date
Wed Jan 01 2025
Journal Name
Asian Pacific Journal Of Cancer Prevention
Quality of Life and Its Associated Factors Among Breast Cancer Women in Iraq: A Cross-Sectional Study
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Publication Date
Wed Apr 30 2025
Journal Name
International Journal Of Environmental Impacts
Analysis of the Effect of Heavy Elements in Polluted Industrial Water and its Environmental Treatment: An Applied Study on the Gas Power Plant/ 1 (Central Region) in Southern Baghdad and its Discharge into the Tigris River
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Water produced from power plants is one of the most important sources of water pollution, especially for areas like Baghdad, Contaminated industrial wastewater is a major environmental challenge due to the rapid growth of industries, leading to increased accumulation of harmful pollutants in water resources, the work is intended to study the impact of water generated from a power plant in the south on the level of heavy metals before and after the treatment process and after its discharge to the Tigris River. Objective is to determine the extent of heavy metals such as iron, copper, chromium, and zinc concentration in water extracted from various points and subsequently study the monthly variations of these elements with a view to assessmen

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Publication Date
Sat Jan 01 2011
Journal Name
College Of Engineering Journal
Study the Effect of Cutting Conditions for turning process on the Machined Surface
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Surfaces quality is one of the most specified customer requirements for machine parts. The major indication of surfaces quality on machined parts is surface roughness. The research aim is to study the cutting conditions and their effects on the surface roughness. This paper utilizes regression models to predict surface roughness over the machining time for variety of cutting conditions in turning. In the experimental part for turning, different types of materials (Aluminum alloy, Copper alloy, and Gray cast iron) were considered with different cutting speed ( ) and feed rate ( ). A mathematical Model depending on statistical-mathematical method between surface roughness (Rz ) and cutting condition ( , ) were derived, for the three materials

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Publication Date
Mon Apr 09 2018
Journal Name
Al-khwarizmi Engineering Journal
Study the Effect of Forming Media on the Hydroforming Process for Copper Tube
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To observe the effect of media of the internal pressure on the equivalent stress distribution in the tube, an experimental study is done by constructing a testing rig to apply the hydraulic pressure and three dies are manufactured with different bulging configurations (square, cosine, and conical). In the other part, ANSYS APDL is generated to analyze the bulging process with hydraulic and rubber (natural and industrial) media. It was found that when the media is a rubber, the stress is decreased about 9.068% in case of cosine die and 5.4439% in case of conical die and 2.8544% in case of square die. So, it can be concluded that the internal pressure in the rubber media is much better than in hydraulic media. Also, the force needed for fo

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Publication Date
Sun Nov 03 2002
Journal Name
University Of Baghdad
Parametric Study Of The Optimum Wing - Canard Configuration For The Swept Forward Fighter
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The aerodynamic characteristics of the forward swept wing aircraft have been studied theoretically and an experimentally investigation for the wake field generated by this configuration have been carried out. Low order panel method with the Dirichlet boundary condition have been used to solve the case of the steady, inviscid and compressible flow. Two different panel method techniques have been employed: the source-doublet and the doublet method. The thickness for the various components was considered in the study. Prandtl-Glauert similarity rule has been used to account for the compressibility effects. Experimentally, a model was manufactured from wood with body length (290mm) and main wing span was (204mm). The primary objective of th

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Publication Date
Thu Nov 19 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
CFD Simulation of Velocity Distribution in a River with a Bend Cross Section and a Cubic Bed Roughness Shape
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Publication Date
Sat Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Effect of TNF-Alpha Gene Polymorphisms At -376 G/A, -806 C/T, and -1031 T/C on The Likelihood of Becoming a Non-Responder to Etanercept in A Sample of Iraqi Rheumatoid Arthritis Patients
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Tumor necrosis factor-alpha (TNF-α) antagonists’ therapy are expensive and has a non-responsive rate between 30% to 40% in rheumatoid arthritis patients. Genetic variation plays a vital role in the responsiveness to this type of therapy.The aim of this study is to investigate if the presence of genetic polymorphism in the TNF-α gene promoter region at locations -376 G/A (rs1800750), -806 C/T (rs4248158), and -1031 T/C (rs1799964) affects rheumatoid arthritis patient's tendency to be a non-responder to etanercept.

Eighty RA patients on etanercept (ETN) for at least six months were recruited from the Rheumatology Unit at Baghdad Teaching Hospital. Based on The European League Against Rheumatism response (EULAR) criteria, patient

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