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Let’s Dock: A Smart Platform for Molecular Docking

Let’s Dock: A Smart Platform for Molecular Docking

Yaruq Jabeen1, Nida Ansari1, Haroon Rasheed1, Muhammad Asif Rasheed1,*, Muhammad Awais2, Muhammad Ibrahim1, Sumaira Kanwal1, Aqsa Khalid3, Manzoor Ahmad Zahid4 and Farrukh Jamil1,*

1Department of Biosciences, COMSATS University, Sahiwal Campus, Punjab
2Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Sialkot, Sialkot
3National University of Sciences and Technology, H-12, Islamabad
4Department of Mathematics, COMSATS University, Sahiwal Campus, Punjab
 
* Corresponding authors: farrukh@cuisahiwal.edu.pk; farrukhccb@gmail.com; asif.resheed@cuisahiwal.edu.pk

ABSTRACT

In the past few years, several docking tools 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 efficient and smart way, a platform has been developed in this study. It is designated “Let’s Dock”. By using this platform, we can perform a docking analysis of several ligands into a protein with AutoDock Vina by just submitting ligands and protein pdb files. Apart from thermodynamic data analysis this platform also calculates descriptors and Lipinski’s rule parameters (Rule of Five) of a ligand by a single click. 

 

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Pakistan Journal of Zoology

August

Vol. 54, Iss. 4, Pages 1501-2001

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