Preferred Language
Articles
/
bijps-1604
A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
...Show More Authors

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.

 

Scopus Crossref
View Publication Preview PDF
Quick Preview PDF
Publication Date
Wed Dec 01 2021
Journal Name
Iraqi Journal Of Veterinary Sciences
Isolation and molecular detection of enterotoxigenic Staphylococcus aureus from raw milk of cows
...Show More Authors

View Publication Preview PDF
Scopus (4)
Crossref (1)
Scopus Crossref
Publication Date
Tue Oct 22 2024
Journal Name
Hemoglobin
Prevalence and Molecular Characterization of β-Thalassemia in Kirkuk Province of Northern Iraq
...Show More Authors

View Publication
Scopus (2)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Mon Nov 14 2022
Journal Name
Biomedicine
Molecular characterization of HBB gene mutations in beta-thalassemia patients of Southern Iraq
...Show More Authors

Introduction and Aim: Beta-thalassemia is a serious inherited genetic disorder and an increasing health burden globally. Beta -thalassemia is caused by genetic globin abnormalities within the hemoglobin beta (HBB) gene. This study aimed to characterize the HBB gene mutations in beta -thalassemia among southern Iraqi patients. Materials and Methods: The study included 30 beta -thalassemia patients referred to the Thi-Qar Center for Genetic Diseases, Iraq and 15 control samples from a random group of apparently healthy individuals. Genomic DNA was isolated from blood sample collected from each individual. The DNA was amplified for specific regions of the HBB gene and the amplified products sequenced. The sequences generated were analysed for

... Show More
View Publication Preview PDF
Scopus (10)
Crossref (2)
Scopus Crossref
Publication Date
Sat Dec 31 2011
Journal Name
Al-khwarizmi Engineering Journal
Back stepping-Based-PID-Controller Designed for an Artificial Pancreas model
...Show More Authors

Artificial pancreas is simulated to handle Type I diabetic patients under intensive care by automatically controlling the insulin infusion rate. A Backstepping technique is used to apply the effect of PID controller to blood glucose level since there is no direct relation between insulin infusion (the manipulated variable) and glucose level in Bergman’s system model subjected to an oral glucose tolerance test by applying a meal translated into a disturbance. Backstepping technique is usually recommended to stabilize and control the states of Bergman's class of nonlinear systems. The results showed a very satisfactory behavior of glucose deviation to a sudden rise represented by the meal that increase the blood glucose

 

... Show More
View Publication Preview PDF
Publication Date
Sun Sep 06 2009
Journal Name
Baghdad Science Journal
Cox proportion hazard model for patients with hepatitis disease in Iraq
...Show More Authors

Cox regression model have been used to estimate proportion hazard model for patients with hepatitis disease recorded in Gastrointestinal and Hepatic diseases Hospital in Iraq for (2002 -2005). Data consists of (age, gender, survival time terminal stat). A Kaplan-Meier method has been applied to estimate survival function and hazerd function.

View Publication Preview PDF
Crossref
Publication Date
Sun Jan 01 2023
Journal Name
Computers, Materials & Continua
Severity Based Light-Weight Encryption Model for Secure Medical Information System
...Show More Authors

View Publication
Scopus (20)
Crossref (35)
Scopus Clarivate Crossref
Publication Date
Fri Feb 28 2025
Journal Name
Journal Européen Des Systèmes Automatisés
Decision-Making Model for Aircraft Landing Based on Fuzzy Logic Approach
...Show More Authors

An aircraft's landing stage involves inherent hazards and problems associated with many factors, such as weather, runway conditions, pilot experiences, etc. The pilot is responsible for selecting the proper landing procedure based on information provided by the landing console operator (LCO). Given the likelihood of human decisions due to errors and biases, creating an intelligent system becomes important to predict accurate decisions. This paper proposes the fuzzy logic method, which intends to handle the uncertainty and ambiguity inherent in the landing phase, providing intelligent decision support to the pilot while reducing the workload of the LCO. The fuzzy system, built using the Mamdani approach in MATLAB software, considers critical

... Show More
View Publication
Scopus (2)
Scopus Crossref
Publication Date
Tue Feb 28 2023
Journal Name
Iraqi Geological Journal
3D Geological Model for Zubair Reservoir in Abu-Amood Oil Field
...Show More Authors

The Zubair reservoir in the Abu-Amood field is considered a shaly sand reservoir in the south of Iraq. The geological model is created for identifying the facies, distributing the petrophysical properties and estimating the volume of hydrocarbon in place. When the data processing by Interactive Petrophysics (IP) software is completed and estimated the permeability reservoir by using the hydraulic unit method then, three main steps are applied to build the geological model, begins with creating a structural, facies and property models. five zones the reservoirs were divided (three reservoir units and two cap rocks) depending on the variation of petrophysical properties (porosity and permeability) that results from IP software interpr

... Show More
View Publication Preview PDF
Scopus (5)
Crossref (1)
Scopus Crossref
Publication Date
Sun Dec 01 2024
Journal Name
Baghdad Science Journal
Densenet Model for Binary Glaucoma Classification Performance Assessment with Texture Feature
...Show More Authors

تعتبر شبكية العين جزءًا مهمًا من العين لأن الأطباء يستخدمون صورها لتشخيص العديد من أمراض العيون مثل الجلوكوما واعتلال الشبكية السكري وإعتام عدسة العين. في الواقع، يعد تصوير الشبكية المجزأ أداة قوية للكشف عن النمو غير العادي في منطقة العين بالإضافة إلى تحديد حجم وبنية القرص البصري. يمكن أن يؤدي الجلوكوما إلى إتلاف القرص البصري، مما يغير مظهر القرص البصري للعين. تعمل تقنيتنا على الكشف عن الجلوكوما وتصنيفه

... Show More
View Publication
Scopus (1)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Fri Nov 20 2020
Journal Name
Journal Of Physical Organic Chemistry
Spectroscopic characterization for new model from Schiff base and its complexes
...Show More Authors
Abstract<p>New complexes have been prepared from the new ligand [2,2′‐(5,5‐dimethylcyclohexane‐1,3‐diylidene)bis(azan‐1‐yl‐1‐ylidene)dibenzoic acid] derived from 5,5‐dimethylcyclohexane‐1,3‐dione and 2‐aminobenzoic acid. Accordingly, its mono and binuclear Mn(II), Co(II), Cu(II), Zn(II), and Cd(II) complexes were prepared. The prepared components have been characterized by various spectroscopic techniques and elemental analysis. The thermal stability of the ligand and its complexes were performed by TGA. It was found that all the complexes have excellent thermal stability and do not contain water molecules within their structure, but the ligand has little stability. Additionally, theor</p> ... Show More
Scopus (35)
Crossref (9)
Scopus Crossref