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 Jan 01 2007
Journal Name
Journal Of Al-nahrain University
STUDY FOR THE GROWTH RATE, VIABILITY AND MORPHOLOGICAL CHANGES OF LEISHMANIA TROPICA IN DIFFERENT CULTURE MEDIA
...Show More Authors

This study included the estimation of growth rate, viability and morphological changes in different culture media (NNN, P-Y, RPMI- 1640, and Panmed). Promastigotes cultured in RPMI-1640 showed maximal growth rate after (2, 4, 6) days of cultivation (27.26 ± 0.05), (172.20 ± 0.1) and (343.81 ± 1.48) million parasites / ml for each day respectively, while P-Y media gave the highest mean of growth rat after (8 and 10) days of cultivation (307.16 ± 1.67) and (303.5 ± 4.96) million parasites / ml for each day respectively. P-Y medium showed the maximal percentage of viability after (2, 4, 6, 8, and 10) days of cultivation (99.76 ± 0.5) %, (98.30 ± 0.17) %, (96.1 ± 0.1) %, (92.5 ± 0.52) % and (87.26 ± 0.05) % for each day respectively.

... Show More
Preview PDF
Publication Date
Sun Jun 05 2011
Journal Name
Baghdad Science Journal
Study the Effect of Scattering and Disperse Radiation on Equivalent Dose Rate for Al & Pb Shields
...Show More Authors

The effects of scattering and secondary radiation generated inside the material on dose equivalent rate where studied using Co60 and Cs137 sources of activity (199.8 , 177.6) MBq , respectively for different thicknesses of Al , Pb and Pb- glass . The results showed that the equivalent rate increases when the effect of scattering was included for Al and Pb shields with cobalt-60 source of energy 1.25 MeV ; and decreases for Pb shield with Cs-137 source of energy 0.662MeV .The results showed also that the atomic number of The material effects the dose equivalent rate . The Pb-glass shield was found to be more efficient in absorption than other shields.

View Publication Preview PDF
Crossref
Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Study of growth curve and morphological change for Trichomonas vaginalis parasite in the tow culture media
...Show More Authors

The objective of this study was shed light for cultivation and maintenance of Trichomonas vaginalis parasite growth after isolated it by vaginal swaps from females suffering vaginitis and abnormal vaginal discharges in these media CPLM and TAB media to detect growth curve, morphological changes and viability of parasite in the two culture media, together with effect of sheep and bovine serum on the growth of it. The results of this studies were showed there was abtaine differences between the two types of media , The maximum growth of parasite was in TAB medium after 72 hours incubation with use of bovine serum, while such growth was maximized after 144 hours incubation with the use of sheep serum. In CPLM medium, a maximum gro

... Show More
View Publication Preview PDF
Crossref
Publication Date
Tue Jun 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Relevance of Budgeting Estimations for Control and Performance Evaluation in Adopting Kaizen: Hypothetical & Empirical Study
...Show More Authors

The kaizen is considered as one of the most important modern techniques which has been adopted by various economics entities especially manufacturing firms and its beginnings return to the middle of the earlier century that has been used by companies like Toshiba, Matsushita Electric, and Toyota. Which realized that these modern techniques would make a total change in the competitive environment and started qualifying and its staff in such away that enables them to go along with this unique environment. The continuous improvement (Kaizen) depends on the small continuous improvements in the product and the production operations during the production stage. Consequently, the research problem is represented in the improperly of the budg

... Show More
View Publication Preview PDF
Publication Date
Sun Jun 21 2020
Journal Name
Baghdad Science Journal
Synthesis of Gold Nanoparticles by using Batch Method and Study its Antibacterial Activity
...Show More Authors

The research involves preparing gold nanoparticles (AuNPs) and studying the factors that influence the shape, sizes and distribution ratio of the prepared particles according to Turkevich method. These factors include (reaction temperature, initial heating, concentration of gold ions, concentration and quantity of added citrate, reaction time and order of reactant addition). Gold nanoparticles prepared were characterized by the following measurements: UV-Visible spectroscopy, X-ray diffraction and scanning electron microscopy. The average size of gold nanoparticles was formed in the range (20 -35) nm. The amount of added citrate was changed and studied. In addition, the concentration of added gold ions was changed and the calibration cur

... Show More
View Publication Preview PDF
Scopus Clarivate Crossref
Publication Date
Wed Jan 15 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Risk management of foreign exchange rates using financial hedging instruments: Applied Analytical Study
...Show More Authors

Management of Foreign Exchange Rate Exposure by Using Financial Hedging An Analytical Empirical Study The main purpose of this Research is to investigate the ability to reduce the  effect  of exchange rate fluctuation on firm value , by usage appropriate hedging strategies to provide the firms force to adopted with complex and highly uncertainty conditions , characteristic of the most of the financial markets  . The field of this study is the giant five Multinational on the world. Nokia, Toyota Motor, Intel , Coca Cola, Microsoft. practical analysis is provide the truth of all study's  hypothesis , and it is reach to many of conclusion, the most important of them is  Stem from unexpected fluctuation on nominal ex

... Show More
View Publication Preview PDF
Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
Assessment of surface water quality using statistical analysis methods: Orontes River (Case study)
...Show More Authors

The study investigates the water quality of the Orontes River, which is considered one of the important water recourses in Syria, as it is used for drinking, irrigation, swimming and industrial needs. A database of 660 measurements for 13 parameters concentrations used, were taken from 11 monitoring points distributed along the Orontes River for a period of five years from 2015-2019, and to study the correlation between parameters and their impact on water quality, statistical analysis was applied using (SPSS) program. Cluster analysis was applied in order to classify the pollution areas along the river, and two groups were given: (low pollution - high pollution), where the areas were classified according to the sources of pollution to w

... Show More
View Publication Preview PDF
Scopus (10)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
Performance Study of AODV, GRP and OSPFv3 MANET Routing Protocols Using OPNET Modeler
...Show More Authors

A Mobile Ad hoc Network (MANET) is a collection of mobile nodes, that forms on the fly a temporary wireless multi-hop network in a self-organizing way, without relying on any established infrastructure. In MANET, a pair of nodes exchange messages either over a direct wireless link, or over a sequence of wireless links including one or more intermediate nodes. For this purpose, an efficient routing protocol is required. This paper introduced performance study of three of MANET protocols (AODV, GRP and OSPFv3). This study was one of the newer studies because wireless communication played an important role in today’s application and the field of mobile ad hoc network becomes very popular for the researchers in the last years. This study w

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Dec 15 2004
Journal Name
Iraqi Journal Of Laser
Interstitial Photocoagulation of Low Anal Fistula using 810 nm Diode Laser: Prospective Study
...Show More Authors

Many conservative sphincter-preserving procedures had been described to be effective in
healing of anal fistula without excision or de roofing.
Objective: To verify the outcome of mere photocoagulation of the fistula tract on healing of low anal
fistula.
Materials and Methods: Using 810nm diode laser, the tracts of low anal fistulae in a cohorts of six male
patients (mean age of 32 yr) had been photocoagulated by retrograde application of laser light through an
orb tip optical fiber threaded in to the tract. Swabs for culture and sensitivity testing were obtained before
and after laser application. Patients were followed up regularly to announce fistula healing.
Results: Mean laser exposure time was 6.6 min., mean

... Show More
View Publication Preview PDF
Publication Date
Mon Feb 14 2022
Journal Name
Journal Of Educational And Psychological Researches
Comparative between Intermediat Stage Art Education Curriculum in Iraq and Egypt Base on the Contemporary Theory
...Show More Authors

The current research aims to analyze the content and and make a comparison based on the theory of art education as an organized cognitive area D.B.A.E. The researcher started by making a comparison followed by analysing the content to design a philosophical framework for content. He used these steps as starting point to study the comparison and some elements of art education due to the modern theories at the third intermediate stage in both Iraq and Egypt in light of the art education trend as an organizing cognitive area.

View Publication Preview PDF