Discover how 3decision supports your SBDD work
Download our detailed feature description document and examples
Small examples are worth more than a thousand words so, how does 3decision® help you in a drug design project?
Have a look at the three use cases, and get a more detailed overview of 3decision® characteristics.
Case 1: Early stages of a new project
Search and download existing structures on the target and homologous proteins.
Find druggable binding sites.
Identify potential off-targets.
Find existing binding chemical matter for your target or related proteins (homologous, off-targets).
Download superimposed structures to use them in modeling tools to build pharmacophores and/or run virtual screening campaigns.
No structures for the target yet? Search for homologous proteins and identify the best templates to build homology models from with some visual aid.
Search similar proteins and extract crystallization parameters.
Modelers might run molecular dynamics with their favorite software and upload different model structures that represent the conformational flexibility of the protein.
Developing in-vitro, in-vivo assays? Check mutations in the binding site between species in 3D to avoid undesired surprises.
Case 2: Lead optimization loop
Upload a new structure: new holo-structure resolved, new docking model, new homology model.
Prepare a 3D scene comparing this new structure with the previous ones in the project to highlight differences with potential interest. E.g: new subpocket opens giving room to add new functional groups to the ligand.
Compare against off-target structures to reveal mutations in the binding site that could be exploited to gain specificity.
Share the scene with your colleagues with a simple URL link that will serve as a basis for discussion to make decisions.
Use the integrated 2-clicks docking feature to quickly test the fitting of the new ideas in the binding site. If more detailed and precise dockings need to be produced, the modeler can take care of this step and upload the models into 3decision restarting the loop.
Some new molecules will be synthesized at some point and new crystal structures will be resolved, restarting this way the loop.
Case 3: Collaborate in drug discovery project
Use 3decision as a common ground for analysis and ideation for drug discovery
Organize structures, models and ligand collections in projects
Find and reuse ideas created in other projects and research programs
Export analyses and data to common data formats
Integrate 3decision into your IT ecosystem via flexible REST APIs
Characteristics
3decision® is different from a molecular modeling software
For starters, 3decision® is not a molecular modeling software and is not meant to replace current tools used by computational chemists. 3decision is a web-based solution that combines a fully annotated and searchable database with a disruptive user interface and state-of-the-art structural analytical tools. It is designed to give molecular modelers, medicinal chemists and structural biologists a common ground for structure-based drug discovery.
In other words, 3decision® is a protein structure registration system, a large-scale structural analytics tool, a protein visualization software, and an ideation platform, all at once.
3decision® includes more than just the PDB
The 3decision® database includes all structures in the Protein Data Bank (PDB) but also contains unique structural Metadata and numerous public data sources, such as SWISS-MODEL’s homology models, ChEMBL’s activity data and a series of sequence annotations. Check out the complete list below.
Data registered in the 3decision® database
Experimental structures: protein and antibodies from the PDB and proprietary data (read more about in-house data below)
3decision’s Pocketome
Protein-Ligand Interactions
Biomolecular sequences: UniProt, proprietary data (optional)
Sequence annotations: protein family domains, functional sites, natural variations, protein class-specific (Antibody, Kinase, GPCR, PDE etc.)
Homology models: SWISS-MODEL
Assay data: ChEMBL
Ligand data: PDBe, ChEMBL
Enrich the 3decision® database with in-house data
In addition to the enhanced public data provided in 3decision®, users can also register their in-house database of experimentally resolved structures. Modeling work such as homology models, docking results and ligand collections can also be registered and persisted in the database. In this way, the structural knowledge created by one team can be retrieved and exploited by other project teams within the organization.