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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
Tue Jul 01 2008
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Analysis of Data Obtained From Chromosomal Studies Performed During the Period from 2000-2007 A Retrospective Study
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Background: Generally, genetic disorders are a leading cause of spontaneous abortion, neonatal death, increased morbidity and mortality in children and adults as well. They a significant health care and psychosocial burden for the patient, the family, the healthcare system and the community as a whole. Chromosomal abnormalities occur much more frequently than is generally appreciated. It is estimated that approximately 1 of 200 newborn infants had some form of chromosomal abnormality. The figure is much higher in fetuses that do not survive to term. It is estimated that in 50% of first trimester abortions, the fetus has a chromosomal abnormality. Aim of the study: This study aims to shed some light on the results of chromosomal studies per

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Publication Date
Wed Jan 10 2018
Journal Name
Al–bahith Al–a'alami
Work Stress Sources of the Communicator in Public Relations “A field study on Governmental Institutions in UAE”.
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This study addressed the work stress sources and level of the communicator in public relations in governmental institutions in the United Arab Emirates. The importance of this study is the lack of studies on work stress of the communicator in public relations. The study aimed to investigate the work stress source Physical, individual, groups, organizational and Professional source which effect on the performance of communicator in public relations. The researcher used the descriptive approach and questionnaire as an essential tool for collecting information. Some of the important results of the study are The communicator in public relations facing stress in work by 42% which affect on his performance by average level. The organizational

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Publication Date
Fri Apr 25 2025
Journal Name
Saudi Endodontic Journal
Insights into periapical inflammatory lesions of the jaws over 30 years in Iraq: A cross-sectional study
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Publication Date
Tue May 23 2023
Journal Name
Journal Of Engineering
Competitive Adsorption of Three Reactive Dyes by Activated Carbon
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In this study three reactive dyes (blue B, red R and yellow Y) in single , binary and ternary solution were adsorbed by activated carbon AC in equilibrium and kinetic experiments. Surface area, Bulk and real density, and porosity were carried out for the activated carbon.
Batch Experiments of pH (2.5-8.5) and initial concentration (5-100) mg/l were carried out for single solution for each dye. Experiments of adsorbent dosage effect (0.1-1)g per 100 ml were studied as a variable to evaluate uptake% and adsorption capacity for single dyes(5, 10) ppm, binary and ternary (10) ppm of mixture solutions solution of dyes. Langmuir, and Freundlich, models were used as Equilibrium isotherm models for single solution. Extended Langmuir and Freun

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Publication Date
Tue Aug 01 2017
Journal Name
International Journal Of Scientific & Engineering Research
Integrated System of Information hiding by Applying Three levels
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MB Mahmood, BN Dhannoon

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Publication Date
Sat Sep 01 2018
Journal Name
International Journal Of Renewable Energy Research
Performance of Wind Turbines at Three Sites in Iraq
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Matching between wind site characteristics and wind turbine characteristics for three selected sites in Iraq was carried out. Site-turbine matching for potential wind power application in Iraq has not yet been well reported on. Thus, in this study, five years’ wind speed data for sites located in Baghdad (33.34N, 44.40E), Nasiriyah (31.05N, 46.25E), and Basrah (30.50N, 47.78E) were collected. A full wind energy analysis based on the measured data, Weibull distribution function, and wind turbine characteristics was made. A code developed using MATLAB software was used to analyse the wind energy and wind turbines models. The primary objective was to achieve a standard wind turbine-site matching based on the capacity factor. Another matching

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
The Usefulness of Mandibular Ramus as an Indicator in Sex Differentiation Using 3D Reconstructed Computed Tomography
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Background: Determination of sex from an unknown human bone is an important role in forensic and anthropology field. The mandible is the largest and hardest facial bone, that commonly resist postmortem damage and forms an important source of information about sexual dimorphism. Mandibular ramus can be used to differentiate between sexes and it also expresses strong univariate sexual dimorphism. This study was undertaken to assess the usefulness of mandibular ramus as an aid in sex differentiation using CT scanning among Iraqi population. Materials and methods: 3D reconstructed computed tomography scanning of 140 Iraqi Arab subjects, (7 0 males and 70 females) were analyzed with their age range from 20-60 years old. The linear measurements w

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
The Direct Gene Injection Using of Egg Yolk Emulsion as Carrier and its Comparison with Liposomes.
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The efficiency of egg yolk emulsion in coating DNA and its delivery across cellular membranes was evaluated in comparison with liposomes DOPE . The murine leukemia viral oncogene v-abl , cloned on pBR322 was used as a DNA substrate for direct injection into mice tissue . the DNA complexes were prepared by mixing the DNA with egg yolk emulsion and liposome . Each was directly injected into mice peritoneal cavity with proper control. The gene delivery was examined phenotypically by blood analysis and cytogenetic analysis . Chromosomal changes were detected in the bone marrow as from the fourth day post inoculation through the eleventh day when chromosomal ring s could be seen . this was accompanied by decrease in the WBC count ,

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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Engineering
Studying the Utility of Using Reed and Sawdust as Waste Materials to Produce Cementitious Building Units
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In this research, the possibility of using waste wooden materials (reed and sawdust) was studied to produce sustainable and thermal insulation lightweight building units , which has economic and environmental advantages. This study is intended to produce light weight building units with low thermal conductivity, so it can be used as partitions to improve the thermal insulation in buildings. Waste wooden materials were used as a partial replacement of natural sand, in different percentages (10, 20, 30, and 40) % . The mix proportions were (1:2.5) (cement: fine aggregate) with w/c of 0.4. The values of 28 days oven dry density ranged between (2060-1693) kg/m3.The thermal conductivity decreased from (0.745 to 0.2

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Publication Date
Sun Nov 23 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of P53, as a marker of apoptosis in Hodgkin’s and Non Hodgkin’s lymphoma of the head and neck region
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Background: Malignant lymphomas represent about 5% of all malignancy of the head and neck region which can involve lymph nodes as well as soft tissue and bone of the maxillofacial region. Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system. Inappropriate apoptosis is a factor in many human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Expression of p53 Proteins in Hodgkin׳s and Non Hodgkin׳s lymphomas suggested that it can help in monitoring of patients and the markers may aid in controlling the progression of lymphoma and detect the degree of aggressiveness of the diseas

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