Collaborative and parallelized immersive molecular docking

Abstract

During docking, protein molecules and other small molecules interact together to form transient macromolecular complexes. Docking is an integral part of structure-based drug design and various docking programs are used for in-silico docking. Although these programs have powerful docking algorithms, they have limitations in the three-dimensional visualization of molecules. An immersive environment would bring additional advantages in understanding the molecules being docked. It would enable scientists to fully visualize molecules to be docked, manipulate their structures and manually dock them before sending to new conformations to a docking algorithm. This could greatly reduce docking time and resource consumption. Being an exhaustive process, parallelization of docking is of utmost importance for faster processing. This paper proposes the use of a collaborative and immersive environment for initially hand docking molecules and which then uses powerful algorithms in existing parallelized docking programs to decrease computational docking time and resources. © 2009 Springer Berlin Heidelberg.