Service / Technology Instance

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The Scipion-Chem Service enables researchers to transform structural information about biological macromolecules into actionable hypotheses for ligand binding and therapeutic development. The service provides a fully integrated environment for binding pocket identification, ligand docking, and virtual screening, allowing users to start with experimentally determined or modeled 3D structures and rapidly generate ranked lists of potential ligands. Users can submit their structures and (optionally) their own compound libraries or access curated public collections to explore new binding sites, prioritise hits, and guide experimental validation.

Input Data

The service requires as input a 3D atomic structure of the target macromolecule. The user may optionally provide a library of small molecules in SMILES format; otherwise, the screening will be performed against a curated set of ~1500 FDA-approved compounds.

Analysis Types

Scipion-Chem offers two main types of analyses:

1. Druggable Pocket Search. This analysis identifies potential ligand-binding sites on the surface of the provided structure. The algorithm detects cavities and evaluates their physicochemical properties—such as hydrophobicity, charge distribution, and geometric accessibility—to estimate their likelihood of accommodating drug-like molecules. The analysis is performed on the static input conformation; no molecular dynamics sampling of alternative conformations is executed at this stage.
2. Drug Binding Prediction. Once pockets are identified, a virtual screening campaign can be launched against the selected pocket(s). Each compound from the chosen drug library is docked onto the target structure, and binding affinities are estimated through molecular docking and scoring protocols. The output includes the predicted binding poses, ranked affinities, and interaction maps between the ligand and the target.

Output and Visualization

Results are fully integrated within the Scipion environment, providing interactive 3D visualization of druggable sites, binding poses, and ranked compound lists. The outputs can be exported for further refinement, such as molecular dynamics simulations or medicinal chemistry optimization.

Use Case

This service enables Instruct users to derive early insights into the druggability of newly solved macromolecular structures and to generate experimentally testable hypotheses about potential ligands. The integration into Scipion ensures traceability, reproducibility, and interoperability with other Instruct pipelines, including those for cryo-EM data processing and atomic model refinement.

Instruments Available:

User Guide

Instruct Centre

Instruct-Madrid

Contacts:

Carlos Oscar Sanchez Sorzano
Spanish National Research Council
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Blanca Elena Benitez Silva
Spanish National Research Council
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