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Related Concept Videos

Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Organization01:13

Protein Organization

Overview
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 Organization01:13

Protein Organization

Overview
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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Updated: May 31, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein-protein complex structure predictions by multimeric threading and template recombination.

Srayanta Mukherjee1, Yang Zhang

  • 1Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.

Structure (London, England : 1993)
|July 12, 2011
PubMed
Summary
This summary is machine-generated.

A new method, COTH, models protein-protein complex structures by combining tertiary structures with complex alignments. This approach significantly outperforms traditional methods for modeling complexes from nonhomologous templates.

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Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) has limited protein-protein complex structures compared to tertiary structures.
  • This scarcity hinders homology-based methods for modeling complex structures.

Purpose of the Study:

  • To develop a novel computational approach, COTH, to enhance protein complex structure modeling.
  • To overcome limitations of homology-based methods by utilizing nonhomologous templates.

Main Methods:

  • A threading-recombination strategy combining tertiary structure templates with complex alignments.
  • Utilizing a modified dynamic programming algorithm for sequence-to-complex template alignment, guided by ab initio binding-site predictions.
  • Employing structural alignments to transfer monomer alignments to a multimeric template framework.

Main Results:

  • COTH successfully identified correct templates for 50% of nonhomologous dimeric proteins after excluding homologous templates.
  • The method significantly outperformed conventional homology modeling algorithms.
  • COTH demonstrated higher accuracy in interface modeling compared to rigid-body docking of unbound structures, albeit with lower coverage.

Conclusions:

  • The threading-recombination approach (COTH) offers a viable strategy for modeling protein complex structures.
  • COTH expands the possibilities for modeling complexes using nonhomologous templates, addressing a key limitation in structural biology.