This section of the user guide introduces the structural search methods available in 3decision. It provides an overview of the concepts and algorithms used to perform these searches.
One of the most distinctive features of 3decision is its nearly complete indexing of known and putative binding sites. 3decision currently includes functionality that allows you to search for similar protein binding sites or subparts of these. This makes it possible to quickly find structurally similar local environments and retrieve information on possible small molecule or peptide fragments that might bind to similar locations. It can also indicate potential off-targets that need to be monitored during compound design cycles within a project.
The feature is described in detail here.
Note: The 3decision Pocket Similarity Search algorithm was revamped and enhanced in version 2.3. For previous 3decision versions, refer to this section of the documentation, that describes the previous Pocket Search algorithm.
Available Tutorials:
Interaction search is a feature to retrieve structures containing a 3D query pattern of interactions. The matching is based on a selection of interactions in a query system. The user can refine interactants and interaction type, interaction length, and orientation tolerance. The returned hits are superimposed on the query and can be displayed in the 3D viewer.
The feature is described in detail here.
Available Tutorials: