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Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Jun 2, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

PRUNE and PROBE--two modular web services for protein-protein docking.

Pralay Mitra1, Debnath Pal

  • 1Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.

Nucleic Acids Research
|May 18, 2011
PubMed
Summary

We developed two web services, PRUNE and PROBE, for protein-protein docking. PRUNE efficiently filters poses, while PROBE refines, scores, and ranks them, improving quaternary structure prediction.

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New Features in Visual Dynamics 3.0
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New Features in Visual Dynamics 3.0

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Related Experiment Videos

Last Updated: Jun 2, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biochemistry

Background:

  • Protein-protein docking is crucial for understanding quaternary structures.
  • Existing docking programs involve pose generation, selection, refinement, and scoring.
  • These tasks are modular, allowing for algorithmic substitution.

Purpose of the Study:

  • To develop modular web services for enhancing protein-protein docking.
  • To introduce PRUNE for efficient pose selection and PROBE for refinement, scoring, and ranking.

Main Methods:

  • Implemented PRUNE using an interface area-based edge-scoring function for pose elimination.
  • Developed PROBE employing a regression model for geometric compatibility and normalized interaction energy for scoring and ranking.
  • Integrated these into modular, publicly accessible web services.

Main Results:

  • PRUNE eliminates over 95% of generated docking poses, significantly reducing computational time.
  • PROBE refines, scores, and ranks the pruned poses.
  • The combined approach increases the likelihood of identifying native-like models.

Conclusions:

  • PRUNE and PROBE offer novel, efficient solutions for protein-protein docking.
  • These web services streamline the prediction of protein quaternary structures.
  • The modular design allows for flexibility and future improvements in docking pipelines.