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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 Mar 06 2016
Journal Name
Baghdad Science Journal
Evaluating the Humoral Immunity and Interleukin 18 Receptor 1 in some Patients with Molluscum Contagiosum Infection
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The molluscum contagiosum virus (MCV) is a dermatotropic poxvirus. The causative agent of molluscum contagiosum (MC) is nonlethal, common and worldwide. Additionally, little inflammation is associated with MC papules. The present study aims to evaluate the immune status of MC patients by measuring the level of immunoglobulins IgG and IgM by using the radial immune diffusion assay (RIA) and the level of interleukin 18 receptor 1 (IL-18R1) by the Enzyme-linked immunosorbent assay (ELISA).The study is conducted during November 2013 to April, 2014 in outpatient clinic of Baquba Teaching Hospital. There are 75 patients, diagnosed with clinical lesions of MCV on different areas of the body, whose age is ranged between 2-50 years including 40(53.

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Publication Date
Wed Nov 18 2020
Journal Name
Medico Legal Update
The Meshing between Epstein Barr Virus Nuclear Antigen-1 and P53 in Iraqi Malignant Breast Tissues
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In Iraq, breast cancer incidence exceeds any other type of cancers and the etiology not understood well.Epstein Barr virus is a gamma herpesviruses and one of carcinogenic viruses that may implicated tobreast carcinogenesis. The nuclear antigen-1 (EBNA-1) protein is the sole EBV antigen that presentedin all tumors related to EBV and plays pivotal roles in carcinogenesis of the virus. Examination appliedby immunohistochemistry (IHC) to detect and demonstrate the correlation between (EBNA-1) and tumorsuppressor protein (P53) expression. The study includes paraffin-embedded tissue blocks of ninety 90malignant breast tissues and thirty 30 normal breast autopsies. EBNA-1 was significantly expressed in 40/90(44.4%) of malignant tissues wh

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Publication Date
Wed Nov 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of mandibular radiomorphometric indices as predictors of osteoporosis in postmenopausal women (Cephalometric reconstructed computed tomographical study)
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Background: Osteoporosis affects almost all of the bones in the female body; the most important one in the facial bone is mandible. Menopause is defined as an absence of the menses for one year. During this time, estrongen, progesterone and ovarian androgens production are diminished due to adult onset ovarian failure which leads to osteoporosis. This study aimed to evaluate the use of computed tomography mandibular morphometric indices for the assessment of pre and postmenopausal osteoporotic women. Subjects and material: This study conducted on 50 Iraqi females divided into 2 groups 20 -30years old as a control group and over50 years old as a study group attending Al-Karkh hospital, Department of Computed Tomography.(each group25 female).

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Publication Date
Sun Dec 04 2011
Journal Name
Baghdad Science Journal
Effect of Gamma Irradiation on Vegetative Growth of three Sugarcane Genotypes (Saccharum officinarum L.) in field
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I n vitro rooting plantlets of three sugarcane genotypes(Co.j.64, Co.j.86 and Missan) were cultured in the field after exposed at different doses of gamma rays (1,2,3,4,) kr. Data of reduction percentage on vegetative growth, roots number, length per plant and their diameter were investigated. Results showed gradual reductions in number of shoots, length and diameter as according to increasing of gamma doses. The reduction percentage in shoot number, length were reached 57.86,70.36 % at 4 kr respectively which have mean number and length per plant reached (9.27 and 55.33 cm) as compared with the control treatment ,While 1 kr caused higher percent in diameter reached 9.69 % with mean of diameter per plant reached 2.57 cm. Mean time , Ge

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Publication Date
Wed Mar 27 2013
Journal Name
Journal Of University Of Babylon
Reduce the required time for measuring the permeability of clayey soils by using new manufactured cell
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Reduce the required time for measuring the permeability of clayey soils by using new manufactured cell

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Publication Date
Fri Dec 31 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
ADSORPTION POTENTIAL FOR A MIXTURE OF CHEMICALLY AND THERMALLY TREATED CLAYS TO REMOVE ORANGE G DYE FROM WASTE-WATER: ADSORPTION POTENTIAL FOR A MIXTURE OF CHEMICALLY AND THERMALLY TREATED CLAYS TO REMOVE ORANGE G DYE FROM WASTE-WATER
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This study examined the adsorption behavior of anionic dye (orange G) from aqueous solution onto the raw and activated a mixture of illite, kaolinite and chlorite clays from area of Zorbatiya (east of Iraq).The chemical treatment involved alkali and acid activation. The alkali activation obtained by treated the raw clay (RC) with 5M NaOH (ACSO) and the acid activation founded by treated it with 0.25M HCl (ACH) and 0.25M  (ACS). The thermal treatment carried out by calcination the produce activated clay at 750oC for acid activation and 105oC for alkali activation. Batch

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Publication Date
Wed Jul 31 2019
Journal Name
Journal Of Educational And Psychological Researches
An Instructional Design According to the constructivism Model for Chemistry Subject and Its Effect on the Life Skill by the Second Intermediate Female Students
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The research aims to identify the effect of teaching-learning design based on the constructivism theory on the life skills of middle stage students. The sample consisted of (60) students from one of the middle schools in Baghdad's governorate. The experimental group and control group consisted of 30 students for each group, the research tool was the life skills scale composed of (78) items. The scale proved its validity and reliability, which was found to be (0.85). The results showed a statistically significant difference in life skills between the two groups of research in favor of the experimental group, which studied the educational design according to models of constructivism theory compared to the usual method of teaching.

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Publication Date
Wed Dec 27 2023
Journal Name
Journal Of Planner And Development
Priorities for the reconstruction of religious buildings in the old city of Mosul using Expert Choice program
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This paper attempts to shed light on the most influential factors in the importance of religious buildings were destroyed because of the recent war due to the control of terrorist gangs of ISIS over the city of Mosul, and to prioritize their reconstruction and their role in reviving the historical center of Mosul.

The research’s problem emerged in the lack of knowledge about the identifying the most influential factors in the importance of religious buildings and utilizing them to prioritize their reconstruction. This study aims to analyze the factors influencing the importance of religious buildings using the Expert Choice software through the Analytic Hierarchy Process (AHP) to reach an analysis of their weights and propose p

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Publication Date
Mon Oct 01 2018
Journal Name
The Saudi Dental Journal
Evaluation of some mechanical properties of a new silicone elastomer for maxillofacial prostheses after addition of intrinsic pigments
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Objective: The approximate life span of a silicone maxillofacial prosthesis is as short as1.5–2 years of clinical service, then a new prosthesis should be fabricated. The most common reasonfor re-making the prosthesis is silicone mechanical properties degradation. The aim of this studywas to assess some mechanical properties of VST-30 silicone for maxillofacial prostheses after addi-tion of intrinsic pigments.Methods: Two types of intrinsic pigments (rayon flocking and burnt sienna); each of them wasincorporated into silicone. One hundred and twenty samples were prepared and split into 4 groupsaccording to the conducted tests (tear strength, hardness, surface roughness, and tensile strengthand elongation percentage) with 30 samples for ea

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Publication Date
Tue Aug 27 2024
Journal Name
Diagnostics
Accuracy of Gingival Crevicular Fluid Biomarkers of MMP8, TIMP1, RANK, RANKL, and OPG in Differentiating Symptomatic and Asymptomatic Apical Periodontitis
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Apical periodontitis (AP) is the most prevalent chronic inflammatory disease of the teeth. Bone resorption dynamics in symptomatic and asymptomatic AP are still unrecognized. This study examined different inflammatory markers within gingival crevicular fluid, including matrix metalloproteinases 8 (MMP8), tissue inhibitors of metalloproteinases 1 (TIMP1), receptor activator of nuclear factor κB (RANK), its ligand (RANKL), and osteoprotegerin (OPG), to be used in comparing symptomatic apical periodontitis (SAP) and asymptomatic apical periodontitis (AAP) versus healthy teeth. Subjects with SAP, AAP, and a control group were recruited and GCF samples were collected by Periopaper strips. Clinical and radiographical measures were used f

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