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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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.
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...

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Related Experiment Video

Updated: May 11, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Adaptive Smith-Waterman residue match seeding for protein structural alignment.

Christopher M Topham1, Mickaël Rouquier, Nathalie Tarrat

  • 1Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France; CNRS, UMR5504, F-31400, Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.

Proteins
|May 31, 2013
PubMed
Summary

POLYFIT is a new algorithm for protein structural alignment. It efficiently identifies matching residues in distantly related proteins, improving alignment accuracy for applications like comparative modeling and protein design.

Keywords:
ASTRALSCOPamino acid residue physical environmentdistance metricligand contactpeptide fragmentrigid-body superpositionstructural overlap

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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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Published on: July 8, 2025

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biochemistry

Background:

  • Accurate protein structural alignment is crucial for understanding protein function and evolution.
  • Existing methods face challenges with distantly related proteins and structural plasticity.

Purpose of the Study:

  • To present the POLYFIT rigid-body algorithm for automated global pairwise and multiple protein structural alignment.
  • To demonstrate POLYFIT's advantages in identifying matching residues and generating longer alignments.

Main Methods:

  • Utilizes Smith-Waterman local alignment for seed equivalences, extended by Needleman-Wunsch dynamic programming.
  • Incorporates evolutionary constraints as residue physical environment strings for overlapped pairs.
  • Employs rigid-body conformational matching of 15-residue fragments for distantly related pairs, accommodating plasticity via parameter adjustment.

Main Results:

  • POLYFIT outperforms 10 widely used aligners on difficult pairwise alignment problems.
  • Demonstrates superior efficiency and robustness in identifying seed positions for distantly related proteins.
  • Generates longer structurally overlapped alignment lengths compared to Matt, SALIGN, and MUSTANG.

Conclusions:

  • POLYFIT offers an efficient and robust solution for protein structural alignment, particularly for distantly related proteins.
  • The algorithm's ability to handle structural plasticity enhances alignment quality.
  • Applications include comparative modeling, protein design, and ligand design, with the tool available via a web server.