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 Jun 30 2004
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The Analysis of a Fixed Bed Absorber Used for the Removal of Pollutants from Water
...Show More Authors

View Publication Preview PDF
Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
Nucleon momentum distributions and elastic electron scattering form factors for 58Ni, 60Ni, 62Ni, and 64Ni isotopes using the framework of coherent fluctuation model
...Show More Authors

The nucleon momentum distributions (NMD) and elastic electron scattering form factors of the ground state for some 1f-2p-shell nuclei, such as 58Ni, 60Ni, 62Ni, and 64Ni
isotopes have been calculated in the framework of the coherent fluctuation model (CFM) and expressed in terms of the weight function lf(x)l. The weight function (fluctuation function) has been related to the nucleon density distribution (NDD) of the nuclei and determined from the theory and experiment. The NDD is derived from a simple method based on the use of the single particle wave functions of the harmonic oscillator potential and the occupation numbers of the states. The feature of the l

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Dec 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
...Show More Authors

New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3 catalyst. The results showed that Re-Ni-Mo/ γ-Al2O3 have more activity in desulfurization than Ni-Mo//γ-Al2O3

... Show More
View Publication Preview PDF
Publication Date
Thu Dec 31 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study of New Re-Ni-Mo/Al2o3 and Conventional Hydrodesulphurization Catalyst
...Show More Authors

New types of hydrodesulfurization (HDS) catalyst Re-Ni-Mo/ γ-Al2O3 was prepared and tested separately with two prepared conventional HDS catalysts (Ni-Mo/ γ-Al2O3 and Co-Mo//γ-Al2O3) by using a pilot plant hydrotreatment unit. Activities of three prepared hydrodesulfurization catalysts were examined in hydrodesulfurization (HDS) of atmospheric gas oil at different temperatures 275 to 350 °C and LHSV 1 to 4 h-1, the reactions conducted under constant pressure 40 bar and H2/HC ratio 500 ml/ml .Moreover, the hydrogenation of aromatic (HAD) in gas oil has been studied. HDS was much improved by adding promoter Re to the Ni-Mo/Al2O3

... Show More
View Publication Preview PDF
Publication Date
Tue Feb 03 2026
Journal Name
Journal Of Baghdad College Of Dentistry
An in-vitro scan electron microscope comparative study of dentine-Biodentine interface
...Show More Authors

Background: Restoration of the gingival margin of Class II cavities with composite resin continues to be problematic, especially where no enamel exists for bonding to the gingival margin. The aim of study is to evaluate the marginal leakage at enamel and cementum margin of class II MOD cavities using amalgam restoration and modern composite restorations Filtek™ P90, Filtek™ Z250 XT (Nano Hybrid Universal Restorative) and SDR bulk fill with different restoratives techniques. Materials and method: Eighty sound maxillary first premolar teeth were collected and divided into two main groups, enamel group and cementum group (40 teeth) for each group. The enamel group was prepared with standardized Class II MOD cavity with gingival margin (1 m

... Show More
View Publication Preview PDF
Publication Date
Mon Jun 03 2019
Journal Name
Rawal Medical Journal
SUPERIOR VERSUS ANTERIOR PLATING OF MIDSHAFT CLAVICLE FRACTURE IN ADULT COMPARATIVE STUDY
...Show More Authors

Clavicle fractures are common injuries in young, active individuals. The majority of the fractures (80% to 85%) occur in the mid-shaft of the bone and account for approximately 2.6% of all fractures. For many years the standard treatment of fracture clavicle was the "figure-of-eight" bandage but several indications for operative fixation, the position of plate fixation for clavicle fracture remains controversial. The aim of this study is to compare between anterio—inferior and anterior-superior plating of mid-shaft displaced clavicle fracture in complications, plate prominence, nonunion, malunion and range of motion. This study is a prospective study conducted in Al-Kindy teaching hospital .A total of 30 patients with fracture mid –sh

... Show More
View Publication Preview PDF
Publication Date
Wed Aug 02 2023
Journal Name
Bionatura
Comparative Study of IgG Between Iraqi Covid-19 Patients and Vaccinated Individuals
...Show More Authors

COVID-19 is a coronavirus disease caused by the severe acute respiratory syndrome. According to the World Health Organization (WHO), coronavirus-2 (SARS-CoV-2) was responsible for 87,747,940 recorded infections and 1,891,352 confirmed deaths as of January 9, 2021. Antibodies that target the Sprotein are efficient in neutralizing the virus. Methodology: 180 samples were collected from clinical sources (Blood and Nasopharyngeal swabs) and from different ages and genders at diverse hospitals in Baghdad / IRAQ between November 5, 2021, to January 20, 2022. All samples were confirmed infected with COVID-19 disease by RT-PCR technique. Haematology analysis and blood group were done for all samples, and Enzyme-Linked Immunosorbent Assay used an Ig

... Show More
Scopus
Publication Date
Tue Nov 01 2022
Journal Name
Reports Of Biochemistry And Molecular Biology
Comparative Study of New Biomarkers in Iraqi DM2 with and without Complications
...Show More Authors

View Publication
Scopus (7)
Crossref (2)
Scopus Crossref
Publication Date
Mon Jan 01 2024
Journal Name
Iranian Journal Of Veterinary Medicine
Comparative Study of Bacterial Contamination in Local Iraqi Sheep and Goats Semen
...Show More Authors

Background: Semen contamination is a detrimental factor in decreasing fertility. Seasonal changes may affect the contamination, too. Objectives: This study was designed to detect semen contamination in ovine and caprine during different seasons. Methods: Six fully mature male sheep and goats were subjected to electro-ejaculator collection twice monthly from February 1, 2022, to January 31, 2023 (Spring, February 1, 2022-April 30, 2022; Summer, May 1, 2022, July 31, 2022; Autumn August 1, 2022, October 31, 2022; Winter November 1, 2022, January 31, 2023), for studying the seasonal effect. A total of 288 semen samples were collected from both species (36 samples from each per season). All samples were subjected to bacterial isolatio

... Show More
View Publication
Scopus (2)
Crossref (1)
Scopus Crossref
Publication Date
Wed Dec 27 2023
Journal Name
Journal Of Planner And Development
The dynamics of the oil industry in shaping land uses: a case study of the Zubair oil field
...Show More Authors

The emergence of oil fields and subsequent changes in adjacent land use are known to affect settlements and communities. Everywhere the industry emerges, there is little understanding about the impact of oil fields on land use in the surrounding areas. The oil industry in Iraq is one of the most important industries and is almost the main industry in the Iraqi economic sector, and it is very clear that this industry is spread over large areas, and at the same time adjoins with population communities linked to it developmentally.

The rapid development and expansion of oil extraction activities in various regions has led to many challenges related to land-use planning and management. Here, the problem of research  arises on th

... Show More
View Publication Preview PDF