Simplify the collaboration and sharing of structural knowledge

 
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Total access

  • Get access to the entire list of 3decision's structural analysis tools and algorithms

  • Exploit the full structural proteome and pocketome available in the public domain

 
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Simplified collaborations

  • Share your results and hypotheses with collaborators in your own group and in other organizations

  • Share 3D views and highlighted results the way you see them

  • Work together with chemists, modelers and biologist - all on the same platform

WHAT CAN I DO IN 3DECISION?

Browse and analyze structural knowledge

  • Browse the structural database using proteins, pockets, and ligands as queries
  • Check the binding profile of the ligands in my pocket of interest across different structures but also on close related proteins.
  • Check the binding site variability among these structures in terms of binding site shape (residues in contact variation) and properties (druggability, volume, etc).
  • Visualize experimental annotations mapped over the sequence and over the structure (e.g. to check if there is some natural variation in the binding site that I should worry about)
  • Verify if a specific animal model is suitable for tests on my target (i.e. check for mutations in the binding site for the specific species)
  • Identify the differences in the binding site to exploit to increase the selectivity for target X compared to the related target Y. 
  • Identify what part of the molecule to modify to gain selectivity for target X.
  • Identify putative off-targets for a specific protein-ligand complex (i.e. search for proteins having a similar pocket, similar pocket sequence, similar binding ligands).
  • Search binding sites containing a sub-pocket of interest (currently in a beta version, still work in progress).
  • Run a sequence search to find suitable templates to build my homology model.

Create and test hypotheses

  • Generate ideas for lead or tool compounds in a new project (i.e. run the target profiling search and get a list of ligands from the potential off-targets to start off).
  • Generate new ideas by exploring and superposing similar binding sites with molecules bound.
  • Create and test hypotheses by docking molecules existing in other structures or by drawing them myself.
  • Test binding hypotheses I have generated elsewhere (e.g. with docking software).
  • Check if the protein-ligand interactions in my binding hypothesis already have been observed in other structures in the database.

Add my own knowledge

  • Annotate a sequence to add my personal notes.
  • Upload my homology models or docking poses to integrate them in the database.

Share

  • Save a particular state of the application and share it via a link with colleagues to further discuss the results.
  • Extract prepared structures  
  • Download superimposed structures and ligands to continue my analysis with other software.

Monthly subscription & Special offer for academic

 

Did you miss our webinar on How to maximize the value of your 3D Biomolecular structures? Watch the replay here!