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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: May 9, 2026

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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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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DockRank: ranking docked conformations using partner-specific sequence homology-based protein interface prediction.

Li C Xue1, Rafael A Jordan, Yasser El-Manzalawy

  • 1Bioinformatics and Computational Biology program, Iowa State University, Ames, Iowa.

Proteins
|July 23, 2013
PubMed
Summary

DockRank improves molecular docking by scoring conformations using predicted interface residues. This novel approach, utilizing partner-specific predictions, significantly enhances the accuracy of identifying near-native protein-protein interactions.

Keywords:
docking scoring functionshomo-interologspartner-specific protein-protein interface residue predictionprotein complex structure predictionprotein-protein dockingsequence homologs

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein-Protein Interactions

Background:

  • Accurate selection of near-native conformations is a critical challenge in molecular docking.
  • Existing scoring functions often struggle to reliably rank docked poses.

Purpose of the Study:

  • To introduce DockRank, a novel scoring function for molecular docking.
  • To evaluate DockRank's performance against state-of-the-art methods using partner-specific interface residue predictions.

Main Methods:

  • Developed DockRank, a scoring approach based on matching docked conformations to predicted interface residues.
  • Utilized partner-specific sequence homology-based protein-protein interface predictor (PS-HomPPI) for residue prediction.
  • Compared DockRank with energy-based scoring functions (ZRank, IRAD) and other interface predictors using Success Rate and Hit Rate metrics.

Main Results:

  • DockRank significantly outperformed ZRank and IRAD, improving Success Rate by up to 4-fold when using partner-specific predictions.
  • DockRank showed substantial improvement (up to 39-fold increase in success rate) over variants using non-partner-specific predictions.
  • Re-ranking ClusPro outputs with DockRank enhanced both Success Rate and Hit Rate.

Conclusions:

  • Partner-specific interface residue information is crucial for accurate docking pose scoring.
  • DockRank offers a superior method for selecting near-native conformations in molecular docking.
  • The DockRank server is publicly available for use.