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Updated: Sep 30, 2025
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
413
ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison
Janez Konc1, Samo Lešnik1, Blaž Škrlj1,2,3
1National Institute of Chemistry, Theory Department, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
Journal of Chemical Information and Modeling
|March 15, 2022
Summary
ProBiS-Dock is a new computational tool that rapidly docks small molecules to proteins, considering both as flexible. This drug discovery software identified novel inhibitors for indoleamine 2,3-dioxygenase 1, a cancer therapy target.
Area of Science:
- Computational chemistry
- Structural biology
- Drug discovery
Background:
- Protein Data Bank (PDB) offers valuable protein-ligand structures.
- Current docking algorithms do not fully utilize ligand information.
- Small molecules and proteins are often treated as rigid entities in docking.
Purpose of the Study:
- To develop ProBiS-Dock, a novel docking algorithm.
- To enable flexible docking of small molecules to proteins.
- To create a new scoring function integrating binding site-specific and statistical approaches.
Main Methods:
- ProBiS-Dock treats proteins and ligands as fully flexible entities.
- Incorporates conformational changes post-ligand binding.
- Utilizes a novel scoring function (ProBiS-Score) and a general statistical scoring function.
Main Results:
- ProBiS-Dock enables rapid small molecule docking to proteins.
- Validated in silico against standard benchmarks.
- Successfully identified novel inhibitors of human indoleamine 2,3-dioxygenase 1 in vitro.
Conclusions:
- ProBiS-Dock leverages PDB data for efficient ligand discovery.
- Demonstrates potential for drug development, particularly for cancer targets.
- Software is available for academic use.
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