NDLI: Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK)

Content Provider	Springer Nature Link
Author	Viji, Shankaran Nehru Balaji, Nagarajan Gautham, Namasivayam
Copyright Year	2012
Abstract	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.
Starting Page	3705
Ending Page	3722
Page Count	18
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	18
Issue Number	8
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2012-03-01
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Alternate binding modes Molecular docking MOLSDOCK Protein - Nucleotide docking Structure based drug design Computer Application in Life Sciences Biomedicine general Life Sciences Molecular Medicine Computer Applications in Chemistry Health Informatics
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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