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
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Molecular study of the relationship of gene expression of some genes with the temperature variation of bacterial growth
...Show More Authors

Pseudomonas aeruginosa is an opportunistic pathogen responsible for serious infections. At least three different exopolysaccharides, alginate, polysaccharide synthesis locus (Psl), and pellicle exopolysaccharide (Pel) make up the biofilm matrix in P. aeruginosa . The effect of temperature on the biofilm formation and gene expression was examined by microtiter plate and real-time quantitative polymerase chain reaction (qRT-PCR). To be able to determine the effect of temperature on biofilm formation and gene expression of P. aeruginosa, 303 clinical and environmental samples were collected. Pseudomonas aeruginosa was isolated from 61 (20.1%) and 48 (15.8%) of the clinical and e

... Show More
View Publication Preview PDF
Scopus (2)
Scopus Crossref
Publication Date
Thu Mar 21 2024
Journal Name
International Development Planning Review
THE EFFECT OF USING A DISABLING FORCE TRAINING TOOL ON WALKING PERFORMANCE: AN ANALYTICAL STUDY OF TIME AND STEP LENGTH IN THE 20 KM WALKING RACE EVENT FOR APPLICANTS
...Show More Authors

Publication Date
Thu Jan 31 2019
Journal Name
Journal Of Engineering
Biological Structure in Contemporary Architecture Work of Architect Caltrava a Model
...Show More Authors

Theoretical trends have appeared Which posed the concept of biological structures in contemporary architecture concept, Spread through the emergence of architectural production that reflect and indicate the nature of the construction structures based on the ideas and principles of biological structures in biological science: Despite the emergence of many architectural proposals that tried to explain the concept in the field of architecture, but it is not dealt with in depth and not given a comprehensive definition: So there was need to search for the concept and its beginning in the biological field as a general framework down to the field of architecture for the purpose of reducing the limits of their search framework T

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Constructing a Scale for the Nine Types of Students Personality: Constructing a Scale for the Nine Types of Students Personality
...Show More Authors

Abstract

The current research aims to construct a scale for the nine types of students’ personality according to Rob Fitzel model. To do this, (162) items were formed that present the nine types of personality with (18) items for each type. To test the validity of the scale, a sample of (584) students of Al-Mustansrya University were chosen. The data of their responses was analyzed by using factor analysis. The findings explored (9) factors as one factor for each type of personality with (12) items for each one. Then, the reliability of the scale was found by using the test-retest method and Alfa Cronbach method.

View Publication Preview PDF
Publication Date
Mon May 01 2017
Journal Name
Energy Procedia
A Coupled Model of the Linear Joule Engine with Embedded Tubular Permanent Magnet Linear Alternator
...Show More Authors

Scopus (16)
Crossref (12)
Scopus Clarivate Crossref
Publication Date
Thu Dec 31 2015
Journal Name
مجلة كلية العلوم الاسلامية
The Secret of Marriage in Christianity A Descriptive Study
...Show More Authors

Marriage is a holly secret in Christian religion .So it id natural that its ceremonies acquired religious form .In general the marriage is contracted by minister of religion in presence of the two parties or by a proxy or presence of parents if it is necessary . And to make the condition of publicity for the marriage ,its procedures must be made before witnesses .Also the minister of religionhave to confirm the agreement of the two parties before beginning the procedures.The marriage ceremonies are made.These procedures are religious traditions that includes praying and make blessings and putting the rings in fingers by thepriest . The marriage is a holly secret performed by the crown pray according to the church religious traditions

Preview PDF
Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
Transitional justice: a study of the concept and mechanisms
...Show More Authors

The concept of transitional justice is newly emerging, as it was mainly associated with addressing issues of serious breaches and abuses of human rights during conflicts and situations resulting from violence and the use of force in societies that are in the process of democratization, as transitional justice aims primarily to restore civil peace and rebuild institutions The state needs multidimensional justice: a judicial system that achieves the rule of law, corrective restoration of the wounds of the past, and a distributive characteristic of the redistribution of wealth.

View Publication Preview PDF
Crossref
Publication Date
Fri Aug 30 2019
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of the English Preposition 'in'
...Show More Authors

The present study aims at analyzing the polysemy of the English preposition in from the cognitive linguistic (CL) point of view using Evans' and Tyler's approach (2003). The perplexity faced by Iraqi second language learners (L2) due to the multi-usages of this preposition has motivated the researcher to conduct this study. Seventy-six second year university students participated in this experimental study. The data of the pre-test and post-test were analyzed by SPSS statistical editor. The results have shown the following: First, a progress of more than (0.05≤) has been detected as far as students' understanding of the multiple usages of the preposition in is concerned. Second, the results of the questionnaire have s

... Show More
View Publication Preview PDF
Publication Date
Thu Sep 10 2020
Journal Name
Journal Of Advances In Mathematics
A Study of The Density Property in Module Theory
...Show More Authors

In this paper, there are two main objectives. The first objective is to study the relationship between the density property and some modules in detail, for instance; semisimple and divisible modules. The Addition complement has a good relationship with the density property of the modules as this importance is highlighted by any submodule N of M has an addition complement with Rad(M)=0. The second objective is to clarify the relationship between the density property and the essential submodules with some examples. As an example of this relationship, we studied the torsion-free module and its relationship with the essential submodules in module M.

Publication Date
Sun Dec 01 2013
Journal Name
Political Sciences Journal
Yemeni political system: a study of the internal variables
...Show More Authors

النظام السياسي اليمني : دراسة في المتغيرات الداخلية

View Publication Preview PDF
Crossref