Journal
JOURNAL OF MOLECULAR MODELING
Volume 18, Issue 8, Pages 3705-3722Publisher
SPRINGER
DOI: 10.1007/s00894-012-1369-4
Keywords
Alternate binding modes; Molecular docking; MOLSDOCK; Protein - Nucleotide docking; Structure based drug design
Categories
Funding
- University Grants Commission
- Department of Science and Technology, Government of India
Ask authors/readers for more resources
Understanding the principles of protein receptor recognition, interaction, and association with molecular substrates and inhibitors is of principal importance in the drug discovery process. MOLSDOCK is a molecular docking method that we have recently developed. It uses mutually orthogonal Latin square sampling (together with a variant of the mean field technique) to identify the optimal docking conformation and pose of a small molecule ligand in the appropriate receptor site. Here we report the application of this method to simultaneously identify both the low energy conformation and the one with the best pose in the case of 62 protein-bound nucleotide ligands. The experimental structures of all these complexes are known. We have compared our results with those obtained from two other well-known molecular docking software, viz. AutoDock 4.2.3 and GOLD 5.1. The results show that the MOLSDOCK method was able to sample a wide range of binding modes for these ligands and also scores them well.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available