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
Mon Oct 13 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Caries severity in relation to oral health knowledge and behavior of third and fifth year dental students / University of Baghdad (A comparative study)
...Show More Authors

Background: Tooth wear is one of the most common problems in the older dentate population which results from the interaction of three processes (attrition, abrasion and erosion) and it affects all societies, different age groups, and all cultures. This study was achieved to evaluate the prevalence and distribution of tooth wear among institutionalized residents in Baghdad city\ Iraq. Subjects and Methods: This survey was accomplished on four private and one governmental institution in Baghdad city. One-hundred twenty three (61 males, 62 females) aged 50-89 years were participated in this study. The diagnosis and recording of tooth wear were according to criteria of Smith and Knight. Results: The prevalence of tooth wear was 100% with a mean

... Show More
View Publication Preview PDF
Publication Date
Sat Dec 31 2011
Journal Name
Al-khwarizmi Engineering Journal
Effect of Mixed Corrosion Inhibitors in Cooling Water System
...Show More Authors

The effect of mixed corrosion inhibitors in cooling system was evaluated by using carbon steel specimens and weight loss analysis. The carbon steel specimens immersed in mixture of sodium phosphate (Na2 HPO4) used as corrosion inhibitor and sodium glocunate (C6 H11 NaO7) as a scale dispersant at different concentrations (20,40, 60, 80 ppm) and at different temperature (25,50,75 and 100)ºC for (1-5) days. The corrosion inhibitors efficiency was calculated by using uninhibited and inhibited water to give 98.1%. The result of these investigations indicate that the corrosion rate decreases with the increase the corrosion inhibitors concentration at 80 ppm and at 100ºC for 5 days, (i.e,

... Show More
View Publication Preview PDF
Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Building a mathematical model of the transportation problem under the dynamics of demand restrictions with practical application
...Show More Authors

Abstract\

In this research we built a mathematical model of the transportation problem  for data of General Company for Grain Under the environment of variable demand ,and situations of incapableness to determining the supply required quantities as a result of economic and commercial reasons, also restrict flow of grain amounts was specified to a known level by the decision makers to ensure that the stock of reserves for emergency situations that face the company from decrease, or non-arrival of the amount of grain to silos , also it took the capabilities of the tanker into consideration and the grain have been restricted to avoid shortages and lack of processing capability, Function has been adopted

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sat Jul 22 2023
Journal Name
Journal Of Engineering
The Influence of Politics on Architectural Thought A Descriptive and Analytical Study of the Effect of Political Ideology on the Achieved Architecture (Berlin City as an Example)
...Show More Authors

The research investigates the political effect and its directions on the architectural thoughts and its achievements and how can this political system affect all fields of life in communities including architectural urban design. The problem of the research lies in the ambiguity effects of the ideological national directions of the Nazi Party on the architecture and urban design of the city of Berlin, then determining the aims of the research to discuss the concepts of politics and architecture and their relation to the way of thinking that plays a role in the process of design that works on property and achieving the suitable urban environments for those communities. After that, the Nazi's party's thought would be studied and analyzed,

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Oct 04 2023
Journal Name
History Of Medicine
Theoretical Biological Activities and Docking studies of new amino-acids Derivatives of Oseltamivir for The Treatment of Coronavirus Disease 2019
...Show More Authors

Antiviral medications may be the best choices for COVID-19 treatment until particular therapeutic treatments become available. Tamiflu (oseltamivir) is a neuraminidase inhibitor licensed for the management and defense against influenza types A and B. Oseltamivir-based medication combinations are currently being used to treat COVID-19 patients who also have the new coronavirus 1 SARS-CoV-2. 1 Oseltamivir administration was related with a less time spent in the hospital, quicker recovery 1 and discharge, and a decreased mortality rate. Docking is a modern computational method for identifying a hit molecule by assessing the binding ability of molecular medicines within the binding target pocket. In this work, we chose 21 ligand compounds that

... Show More
Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Engineering
Determination of Mono-crystalline Silicon Photovoltaic Module Parameters Using Three Different Methods
...Show More Authors

For modeling a photovoltaic module, it is necessary to calculate the basic parameters which control the current-voltage characteristic curves, that is not provided by the manufacturer. Generally, for mono crystalline silicon module, the shunt resistance is generally high, and it is neglected in this model. In this study, three methods are presented for four parameters model. Explicit simplified method based on an analytical solution, slope method based on manufacturer data, and iterative method based on a numerical resolution. The results obtained for these methods were compared with experimental measured data. The iterative method was more accurate than the other two methods but more complexity. The average deviation of

... Show More
View Publication Preview PDF
Publication Date
Tue Mar 26 2024
Journal Name
Scientific Reports
An in vitro assessment of the residual dentin after using three minimally invasive caries removal techniques
...Show More Authors
Abstract<p>To evaluate the efficiency and effectiveness of three minimally invasive (MI) techniques in removing deep dentin carious lesions. Forty extracted carious molars were treated by conventional rotary excavation (control), chemomechanical caries removal agent (Brix 3000), ultrasonic abrasion (WOODPECKER, GUILIN, China); and Er, Cr: YSGG laser ablation (BIOLASE San Clemente, CA, USA). The assessments include; the excavation time, DIAGNOdent pen, Raman spectroscopy, Vickers microhardness, and scanning electron microscope combined with energy dispersive X-ray spectroscopy (SEM–EDX). The rotary method recorded the shortest excavation time (p < 0.001), Brix 3000 gel was the slowest. DIAGNOdent pen va</p> ... Show More
View Publication Preview PDF
Scopus (7)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Fri Jan 01 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Molecular study to the fungus Neosetophomasamarorum was isolated from Al Chabaish marsh, South of Iraq
...Show More Authors

IA Ali, FK Emran, DF Salloom, Annals of the Romanian Society for Cell Biology, 2021

View Publication
Publication Date
Thu Aug 13 2020
Journal Name
Asia Pacific Journal Of Molecular Biology And Biotechnology
The anticancer molecular mechanism of Carnosol in human cervical cancer cells: An in vitro study
...Show More Authors

Carnosol, a phenolic diterpene, is one of the effective anticancer agents naturally occurring in rosemary, sage, parsley, and oregano. The chemoresistance problem increased with the routinely used chemotherapy. Therefore, the efforts to find a substitute with safe and low cost have become crucial worldwide. The current study attempts to inspect the anticancer molecular mechanisms of Carnosol on modulating up- and down- regulation of multiple genetic carcinogenesis pathways. The cytotoxicity of Carnosol on Hela cells was evaluated by MTS assay. Flow cytometry was used to assess apoptosis and cell cycle arrest. The apoptotic morphological changes were obvious by dual apoptosis assay. The differential gene expression after treatment wi

... Show More
View Publication
Scopus Crossref
Publication Date
Mon May 21 2007
Journal Name
Journal Of Planner And Development
Using the Input - Output Model in building the economic plan using the computer
...Show More Authors

The origin of this technique lies in the analysis of François Kenai (1694-1774), the leader of the School of Naturalists, presented in Tableau Economique. This method was developed by Karl Marx in his analysis of the Departmental Relationships and the nature of these relations in the models of " "He said. The current picture of this type of economic analysis is credited to the Russian economist Vasily Leontif. This analytical model is commonly used in developing economic plans in developing countries (p. 1, p. 86). There are several types of input and output models, such as static model, mobile model, regional models, and so on. However, this research will be confined to the open-ended model, which found areas in practical application.

... Show More
View Publication Preview PDF