Search for Molecular docking

Structure Based Virtual Screening and Molecular Docking Studies for Identification of Allosteric Inhibitors against Zika Virus Protease NS2B-NS3

Musrrat Fatima, Muhammad Saad Khan, Hamid Rashid, Asim Mehmood, Sumaira Kanwal, Muhammad Asif Rasheed and Farrukh Jamil*

Targeted Based Drug Designing of Pimarane Diterpenes as Potential Inhibitors of New Delhi-Beta-Lactamase

Syed Aun Muhammad¹, Muhammad Soaib Said², Shams Ur Rehman², Muhammad Dawood², Muneer Ahmed Qazi³ and Nighat Fatima^2,*

...thein B) to the NMD-1 by molecular docking. A computational ligand-target docking approach was used to analyze structural complexes of enzyme target with diaportheins. Auto Grid model showed the most energetically favorable binding mode of natural compounds to beta-lactamase. Docked energies for diaporthein A and B were -8.02 and -8.41 kcal/mol, respectively. These outcomes revealed that these ligands could be potential drugs to treat infectious diseases.

Cytotoxicity and Molecular Docking Studies of a Novel Enaminone and its Cadmium (II) Complex

Rahila Huma^1,2, Tariq Mahmud^1,*, Rubina Munir², Sana Javaid Awan³,Kiran Iftikhar⁴ and Mufakkira-Tul-Islam⁵

Conformational Changes in Wild Type KRAS Induced by Two Novel Variants p.E31K and p.G138V

Bibi Nazia Murtaza^1,2, Azhar Qayum³, Shamaila Inayat Nadeem¹, Naif Awdh Al-Maliki⁴, Abdulaziz Alamri⁴ and Abdul Rauf Shakoori^2,5,*

...y in silico analysis and molecular docking of variants with GTP. MutationTaster was used for functional analysis of genetic variants and three-dimensional structure of mutant proteins were built by Swiss-Model and were further subjected to structural alignment and stability studies by I-Mutant Suite and DUET server. Both variants were predicted as ‘disease causing’ and protein stability analysis revealed p.G138V to be more destabilizing variant tha...

Studies on the Recombinant Production in E. coli and Characterization of Pharmaceutically Important Thermostable L-Asparaginase from Geobacillus thermodenitrificans

Muhammad Shahid Nadeem*, Maryam A. Al-Ghamdi and Jalaluddin Azam Khan

Single Nucleotide Polymorphism Induces a Positive Selection Pressure at Gag-Pol Sites in Human Immunodeficiency Virus Favoring Drug Resistance Mutations

Amreen Zahra¹, Mushtaq A. Saleem¹*, Hasnain Javed², Muhammad Azmat Ullah Khan³, Muhammad Naveed¹ and Abdul Rauf Shakoori⁴

... inhibitor, was used for molecular docking to reveal the drug resistance sites among the isolates under investigation. However, strikingly the binding energies resulted were -7.9 kcal/mol for Pol and -5.7 kcal/mol in Gag that predicted that SNPs in the Pol gene could be one of the reasons for drug resistance and the primary site of mutations progressing the onset of infection. These computational strategies will thus help in performing large scale studies and ...

Ameliorative Effect of Almond Oil Against Doxorubicin-Induced Cardiotoxicity in Mice Via Downregulation of TLR4 Gene Expression, Lowering NF-κB and TNF-α Levels

Doaa Sh. Mohamed1, Nema S. Shaban2 , Mai M. Labib3, Olfat Shehata4

...ities were elucidated by molecular docking studies. Treatment with almond oil attenuated lipid peroxidation, improved superoxide dismutase (SOD) activities that are associated with doxorubicin administration. Also almond oil considerably modulated the gene expression of toll like receptor 4 (TLR4) and lowers the serum levels of both nuclear factor κB (NF-κB) and tumor necrosis factor α (TNF-α). The elevated levels of Creatine Kinase - M...

Let’s Dock: A Smart Platform for Molecular Docking

Yaruq Jabeen¹, Nida Ansari¹, Haroon Rasheed¹, Muhammad Asif Rasheed^1,*, Muhammad Awais², Muhammad Ibrahim¹, Sumaira Kanwal¹, Aqsa Khalid³, Manzoor Ahmad Zahid⁴ and Farrukh Jamil^1,*

... have been developed for molecular dockings such as LeDock, rDock, AutoDock Vina, AutoDock, UCSF DOCK, GOLD, Glide, Surflex-Dock, LigandFit and MOE-Dock. Among these, AutoDock Vina has been widely used by academia for molecular docking. This tool performs docking of a ligand into a protein by seven steps. For docking analysis of several ligands, AutoDock Vina is a time-consuming tool. In order to make AutoDock Vina more effi...