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Related Concept Videos

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...
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 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.
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...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

Evaluation of multiple protein docking structures using correctly predicted pairwise subunits.

Juan Esquivel-Rodríguez1, Daisuke Kihara

  • 1Department of Computer Science, College of Science, Purdue University, West Lafayette, IN 47907, USA.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

Accurate prediction of protein complexes is crucial. A new metric, the fraction of correctly predicted pairs (fpair), better evaluates multiple protein docking accuracy than global measures like RMSD.

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein complexes are vital for cellular functions.
  • Computational prediction of protein complexes is a key bioinformatics challenge.
  • Evaluating the accuracy of multiple protein docking methods requires robust metrics.

Purpose of the Study:

  • To investigate appropriate accuracy metrics for multiple protein complex models.
  • To determine how accurate structural models need to be for biological insight.
  • To propose a novel evaluation metric for multiple protein docking.

Main Methods:

  • Generated protein complex models (decoys) of varying accuracy using the Multi-LZerD pipeline.
  • Analyzed three multi-chain complexes (3, 4, and 6 chains).
  • Assessed decoys based on correctly predicted pairwise chain conformations.

Main Results:

  • Correct pairwise chain orientations were found even in models with high global RMSD.
  • Local measurements, like correctly predicted pairs, offer better evaluation than global RMSD.
  • Proposed 'fpair' (fraction of correctly predicted pairs) as a new metric.

Conclusions:

  • 'fpair' provides a more informative evaluation of multiple protein docking accuracy.
  • Local interface accuracy is critical for assessing biological relevance of protein complex models.
  • The proposed fpair metric aids in evaluating computational predictions of multi-chain protein complexes.