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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Related Experiment Video

Updated: Sep 30, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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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
PubMed
Summary
This summary is machine-generated.

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.

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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.