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A Protocol for Computer-Based Protein Structure and Function Prediction
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Current successes and remaining challenges in protein function prediction.

Constance J Jeffery1

  • 1Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States.

Frontiers in Bioinformatics
|August 14, 2023
PubMed
Summary
This summary is machine-generated.

Predicting protein function is crucial for understanding genomes, but over 30% of protein-coding genes remain unknown. Recent advancements improve prediction, yet challenges persist in annotating diverse and complex protein functions.

Keywords:
databasesfunction predictionprotein functionprotein structurestructure and function

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Significant progress has been made in protein function prediction, aiding the annotation of protein sequences.
  • However, a substantial portion (over 30%) of protein-coding genes across sequenced genomes still have unknown functions.
  • Protein functions are diverse, encompassing catalysis, binding, and structural roles, with some being inherently difficult to predict.

Purpose of the Study:

  • To review recent developments in computational methods for predicting protein functions.
  • To highlight the persistent challenges in accurately annotating protein sequences and their roles.
  • To discuss complexities arising from multifunctional proteins and subtle sequence/structure-function relationships.

Main Methods:

  • Review of recent literature on protein function prediction algorithms and techniques.
  • Analysis of factors contributing to prediction difficulties, including protein complexity and data limitations.
  • Discussion of emerging computational approaches and their potential impact on functional genomics.

Main Results:

  • Improvements in protein function prediction have enhanced genome annotation success rates.
  • Key challenges remain, particularly for proteins with multiple functions or subtle functional distinctions.
  • Physical features and complex sequence/structure relationships pose significant hurdles for accurate prediction.

Conclusions:

  • Continued research into advanced prediction methods is essential for comprehensive genome annotation.
  • Addressing the complexities of protein multifunctionality and structure-function relationships is critical.
  • Future efforts should focus on developing more robust and nuanced computational tools for protein function prediction.