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Related Concept Videos

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...
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 Organization01:24

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

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Updated: Jun 23, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic

Srayanta Mukherjee1, Yang Zhang

  • 1Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA.

Nucleic Acids Research
|May 16, 2009
PubMed
Summary
This summary is machine-generated.

A new algorithm, MM-align, accurately aligns protein complex structures without needing sequence information. This method enhances protein-protein interaction studies by improving structural comparisons and identifying relevant biological pairs.

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Last Updated: Jun 23, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

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09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Structural comparison of protein complexes is crucial for understanding protein-protein interactions.
  • Existing methods may not be optimal for complex, multi-chain structures.

Purpose of the Study:

  • To develop a novel algorithm, MM-align, for sequence-independent alignment of protein complex structures.
  • To improve the accuracy and efficiency of structural comparisons for multi-chain protein complexes.

Main Methods:

  • MM-align utilizes a modified Needleman-Wunsch dynamic programming algorithm.
  • It aligns multiple chains simultaneously, preventing cross-chain alignments and incorporating interface-specific weighting.
  • The algorithm was tested on a large benchmark dataset of protein complex pairs.

Main Results:

  • MM-align demonstrated significantly higher alignment accuracy compared to extensions of monomer alignment programs, as measured by TM-score.
  • The algorithm is approximately two times faster than TM-align.
  • Enhanced alignment of interface residues aids in identifying biologically relevant complex pairs.

Conclusions:

  • MM-align provides an accurate and efficient method for sequence-independent structural alignment of protein complexes.
  • The algorithm advances the study of protein-protein interactions by enabling better structural comparisons.
  • Interface-specific enhancements improve the identification of functionally significant protein complexes.