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
Sun Mar 01 2020
Journal Name
Journal Of Engineering
Three-Dimensional Explicit Finite Element Simulation of Piled-Raft Foundation
...Show More Authors

This paper aims to validate a proposed finite element model to be adopted in predicting displacement and soil stresses of a piled-raft foundation. The proposed model adopts the solid element to simulate the raft, piles, and soil mass. An explicit integration scheme has been used to simulate nonlinear static aspects of the piled-raft foundation and to avoid the computational difficulties associated with the implicit finite element analysis.

The validation process is based on comparing the results of the proposed finite element model with those of a scaled-down experimental work achieved by other researchers. Centrifuge apparatus has been used in the experimental work to generate the required stresses to simulate t

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Tue Dec 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance Evaluation of Three Phase Spray Direct Contact Heat Exchanger
...Show More Authors

 

The present investigation deals with experimental study of three-phase direct-contact heat exchanger, for water-Freon R11 system, where water is the continuous phase (liquid) and Freon R11 (liquid-gas) is the dispersed phase. The test section consisted of a cylindrical Perspex column with inner diameter 8cm and 1.2m long, in which, water was to be confined. Liquid Freon R11 drops were injected into the hot water filled column, through a special design of distributors at the bottom of the column. The liquid Freon R11 drops rose on their way up and evaporated into two-phase bubbles at atmospheric pressure. The study was devoted to express the effect of process variables such as c

... Show More
View Publication Preview PDF
Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Antibacterial Activity of Three Algal Genera against some Pathogenic Bacteria
...Show More Authors

In the current study, three types of algae namely Tetradesmus nygaardi (MZ801740), Scenedesmus quadricauda (MZ801741) and Coelastrella sp (MZ801742) were extracted by 95% ethanol and hexane against two types of gram positive and two types of gram negative bacteria by wells diffusion methods. Eleven concentrations from the extract of algae (2, 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50 mg/ml) were utilized. It was noticed that ethanolic extraction was more effective than hexane in Scenedesmus quadricauda than the two other mentioned algal species against all pathogenic bacteria, Acintobacter baumanii (ATCC: 19606), Klebsiella pneumonia (ATCC: 13883) Enterococcus faecalis (ATCC: 29212) and Staphylococc

... Show More
View Publication Preview PDF
Scopus (16)
Crossref (4)
Scopus Clarivate Crossref
Publication Date
Fri Sep 15 2023
Journal Name
Sumer 2
Response of Three Citrus Rootstocks to Organic and Biological Fertilizers
...Show More Authors

This study was conducted in a lath house, Dept of Hort. and Landscape, College of Agricultural Engineering Sciences, Univ. During the 2021 growing season, Baghdad will investigate the influence of organic and Biological fertilizers on three Citrus rootstocks' growth and leaf mineral content. The first factor is the addition of liquid organic fertilizers Vit-Org (O) at three levels without addition (O0), soil addition at 10 ml.L-1 (O10) and soil addition at 20 ml.L-1 (O20). The second factor is the addition of nitrogen-fixing bacteria without addition (N1), add 30 ml.Transplant-1 of Azotobacter chroococcum (N2) and add 30 ml.Transplant-1 of Azospirillum brasilemse (N3). The third factor is three citrus rootstocks: sour orange (R1), R

... Show More
View Publication
Scopus (3)
Crossref (5)
Scopus Crossref
Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A comparison between Bayesian Method and Full Maximum Likelihood to estimate Poisson regression model hierarchy and its application to the maternal deaths in Baghdad
...Show More Authors

Abstract:

 This research aims to compare Bayesian Method and Full Maximum Likelihood to estimate hierarchical Poisson regression model.

The comparison was done by  simulation  using different sample sizes (n = 30, 60, 120) and different Frequencies (r = 1000, 5000) for the experiments as was the adoption of the  Mean Square Error to compare the preference estimation methods and then choose the best way to appreciate model and concluded that hierarchical Poisson regression model that has been appreciated Full Maximum Likelihood Full Maximum Likelihood  with sample size  (n = 30) is the best to represent the maternal mortality data after it has been reliance value param

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Use Simulation To Differentiate Between Some Modern Methods To the Model GM(1,1) To Find Missing Values And Estimate Parameters With A Practical Application
...Show More Authors

Abstract

       The grey system model GM(1,1) is the model of the prediction of the time series and the basis of the grey theory. This research presents the methods for estimating parameters of the grey model GM(1,1) is the accumulative method (ACC), the exponential method (EXP), modified exponential method (Mod EXP) and the Particle Swarm Optimization method (PSO). These methods were compared based on the Mean square error (MSE) and the Mean Absolute percentage error (MAPE) as a basis comparator and the simulation method was adopted for the best of the four methods, The best method was obtained and then applied to real data. This data represents the consumption rate of two types of oils a he

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Jan 04 2024
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Performance Auditing Process Pursuant to the Programs and Policies Guide in improving the health insurance Prosperity: applied research in the Iraqi General Insurance Company
...Show More Authors

Abstract

              The research’s goal lies in demonstrating the impact of the Federal Financial Supervision Endowment through the process of auditing the performance of the entities subject to its audit as to improve the performance of these entities, especially if the performance audit method is one of the newly applied methods that are compatible with the standards issued by the International Organization of Financial Supervision and Accounting Institutions which is the method of auditing performance according to the performance evaluation guide for programs and policies issued by the Federal Office of Financial Supervision.

 T

... Show More
View Publication Preview PDF
Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
The study of water quality changes using GIS and remote sensing for Tigris River through Salah Al-Din province, Iraq
...Show More Authors

The most significant water supply, which is the basis of agriculture, industry and human and wildlife needs, is the river. In order to determine its suitability for drinking purposes, this study aims to measure the Water Quality Index (WQI) of the Tigris River in the Salah Al-Din Province (center of Tikrit), north of Baghdad. For ten (9) physio-chemical parameters, namely turbidity, total suspended sediments, PH, electrical conductivity, total dissolved solids, alkalinity, chloride, nitrogen as nitrate, sulphate, and then transported for examination to the laboratory, water samples were collected from 13 locations along the Tigris river. Using the weighted arithmetic index method, the WQI was measured and found to be 105,87 in up-stream, wh

... Show More
View Publication
Scopus (2)
Crossref (1)
Scopus Crossref
Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
The Combined Action of Zeolite and Chlorinated Rubber as Flame Retardants for Epoxy Resin
...Show More Authors

In this work , the effect of chlorinated rubber (additive I), zeolite 3A with chlorinated rubber (additive II), zeolite 4A with chlorinated rubber (additiveIII), and zeolite 5A with chlorinated rubber (additive IV), on flammability for epoxy resin studied, in the weight ratios of (2, 4, 7,10 & 12%) by preparing films of (130x130x3) mm in diameters, three standard test methods used to measure the flame retardation which are ; ASTM : D-2863 , ASTM : D-635 & ASTM : D-3014. Results obtained from these tests indicated that all of them are effective and the additive IV has the highest efficiency as a flame retardant.

View Publication Preview PDF
Crossref
Publication Date
Wed Jan 01 2025
Journal Name
Smart Innovation, Systems And Technologies
The Effect of Bulgarian Bag Exercises to Develop Explosive Force, Characterized by Speed and Accuracy of the Spiking Performance of Volleyball Players
...Show More Authors

The purpose of this study is to develop and assess the effectiveness of exercises using heavy and hanging ropes for handball players, focusing on enhancing specific physical abilities and shooting accuracy. The research addresses the gap in training methodologies by comparing the effects of heavy rope exercises versus hanging rope exercises. An experimental design was used in two equal groups, besides pre-testing and post-testing. The study involved 16 players from the School of Handball for the season 2022–2023. The sample included 14 players, who were then randomly divided into two experimental groups of 7 each. The first group performed heavy rope exercises, while hanging rope exercises were included in the plan of the second group. Th

... Show More
View Publication
Scopus Crossref