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Related Experiment Video

Updated: Jun 24, 2026

Evaluation of Protein&#8211;Protein Interactions using an On-Membrane Digestion Technique
07:07

Evaluation of Protein–Protein Interactions using an On-Membrane Digestion Technique

Published on: July 19, 2019

PROCAIN: protein profile comparison with assisting information.

Yong Wang1, Ruslan I Sadreyev, Nick V Grishin

  • 1Biomedical Engineering Program, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

Nucleic Acids Research
|April 10, 2009
PubMed
Summary
This summary is machine-generated.

PROCAIN is a novel method for detecting remote protein sequence homology by analyzing multiple sequence alignments (MSAs). It combines vertical and horizontal sequence context for sensitive protein structure and function inference.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Accurate inference of protein structure, function, and evolution relies on detecting remote sequence homology.
  • Multiple sequence alignments (MSAs) capture evolutionary patterns crucial for sensitive homology detection.

Purpose of the Study:

  • To introduce PROCAIN, a new method for multiple sequence alignment (MSA) comparison.
  • To enhance the detection of remote sequence homology for improved protein analysis.

Main Methods:

  • PROCAIN combines 'vertical' MSA context (substitution constraints) with 'horizontal' context (residue patterns across positions).
  • It utilizes a profile methodology and measures for horizontal MSA pattern similarity.
  • Secondary structure (SS) prediction is incorporated to further refine performance.

Main Results:

  • PROCAIN achieves homology detection quality comparable to advanced methods like hidden Markov models (HMMs) and SS prediction.
  • Incorporating SS information enhances PROCAIN's performance beyond current state-of-the-art tools.
  • The method successfully detects subtle homology between evolutionarily distant, structurally similar protein domains.

Conclusions:

  • PROCAIN offers a sensitive and effective approach for remote sequence homology detection.
  • The method has significant potential for improving protein structure and function predictions.
  • PROCAIN provides valuable tools and databases for the scientific community.