Creates the 3D structure of DNA from the DNA sequence along with an intercalation site, and docks a ligand at the intercalation site. Intercalate is a state-of-the-art, robust and dedicated drug-DNA intercalation methodology. This method also predicts the best binding mode of ligand efficiently through binding free energy estimations in an automated mode. Intercalate methodology holds the potential for the identification of new ligand molecules intercalating to DNA non-covalently. A webserver is also created based on the proposed methodology and is made freely accessible. The webserver contains both the datasets, all the structures used in developing the methodology and a guide to its usage.
Department of Chemistry & Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi, India
Intercalate funding source(s)
This work is supported by the Department of Biotechnology, Govt. of India.