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3decision for Molecular Modelers


3decision for Molecular Modelers


3decision facilitates collaboration in drug discovery project

3decision allows you to perform advanced searches of protein & ligand 3D structural data and analyze the results with a set of integrated tools. The user interface is adapted to both beginners and advanced users and lets the whole drug discovery team to generate, test and share ideas.

To be a bit more specific, here are some typical use-cases for Molecular Modeler user profile:    

  • Get an overview of all structural knowledge on your target (public and proprietary data)

  • Search for similar ligand-protein interactions in other protein families or projects

  • Identify off-targets and new ideas through large-scale pocket similarity search

  • Assess docking poses based on protein-ligand interaction statistics

  • Generate ideas on how to modify your compound to increase the selectivity

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

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3decision for Medicinal Chemists


3decision for Medicinal Chemists


Medicinal chemistry ideas

Quickly generate and test new drug design hypotheses within 3decision

The 3decision user interface allows you to easily use structure-based methods to generate and test your ideas. A common workflow looks like this:

  • visualize all compounds that bind to your target and similar binding sites (homologs, off-targets etc.)

  • compare their binding mode with an automated structure overlay

  • create new compounds directly in a 2D-sketcher

  • test your ideas with a simple quick-docking

  • share your new hypothesis through different collaborative features

Ideation in medicinal chemistry

Discover the most common use-cases

  • Perform ligand design and docking

  • Superpose two binding sites in one click

  • Retrieve all compounds that are bound to your target

  • Gather a list of compounds that bind to similar binding pockets

  • Search for compounds that bind with similar interactions

  • Share your design ideas with the project team

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3decision for Structural Biologists


3decision for Structural Biologists


3decision facilitates collaboration in drug discovery project

3decision allows you to perform advanced searches of protein & ligand 3D structural data and analyze the results with a set of integrated tools. The user interface is adapted to both beginners and advanced users and lets the whole drug discovery team to generate, test and share ideas.

To be a bit more specific, here are some typical use-cases for Structural Biologist user profile:

  • Share intermediate states of a resolved structure before publishing the final version

  • Centralize and standardize the storage of structures resolved by X-ray crystallography, NMR or cryo-EM

  • Register and share structure PDF reports directly via the user interface

  • Compare resolved protein-ligand interactions to large-scale statistics

  • Visualize electron density maps

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3decision Facilitates Collaboration


3decision Facilitates Collaboration


3decision facilitates collaboration in drug discovery project

3decision allows you to perform advanced searches of protein & ligand 3D structural data and analyze the results with a set of integrated tools. The user interface is adapted to both beginners and advanced users and lets the whole drug discovery team to generate, test and share ideas.

To be a bit more specific, here are some typical use-cases for team members:

  • 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

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3decision is not a Molecular Modeling software


3decision is not a Molecular Modeling software


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.

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3decision includes more than the PDB


3decision includes more than the PDB


3decision includes more than just the PDB

More than just protein structures

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 (optional)

  • 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

Access to the entire structurally resolved pocketome

The pocketome is one of 3decision’s unique features. All pockets, both ligand-bound and un-occupied pockets, have been detected and registered in 3decision. Each pocket is characterized by a druggability score and a series of additional descriptors.

enhanced pocketome

The advanced search & analytics tools within the user interface allow the scientist to identify similar pockets and binding sites. This feature is valuable for idea generation and identification of putative off-targets.

The user can also to tap into the augmented pocketome via 3decision’s structure-to-sequence mapping. The pocket sequence can easily be compared to the canonical sequence of a structurally un-resolved protein homolog. The user can get unique insights into the binding-site differences and thus assess the ligandibility of the unresolved pocket.

State-of-the-art tools for advanced search

3decision’s web-based user interface pushes the advanced search very far. In addition to the classical text format (PDB codes, gene names, SMILES strings, protein sequences, etc.), the user can also use a pocket to search for structural data.

A sketcher is also available and allows for substructure- and multiple similarity searches.

On the Biologics-side, the user can perform an advanced search for CDR and Framework motifs in Heavy or Light chains.

Enrich the database with in-house data

In addition to the enhanced public data provided in 3decision, users with an Enterprise license 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.

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Your 3decision is unique


Your 3decision is unique


Your 3decision is unique

By default, the entire Protein Data Bank (PDB) is registered in the database. If you use the Enterprise solution, you can safely register your in-house structures via a programmatic bulk import or via the user interface.

3decision is a knowledge-based software that allows you to register and organize other types of structural knowledge, such as homology models, docking results, and ligand collections.