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Updated: Jun 3, 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 sequence comparison and fold recognition: progress and good-practice benchmarking.

Johannes Söding1, Michael Remmert

  • 1Gene Center and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, Munich, Germany. soeding@genzentrum.lmu.de

Current Opinion in Structural Biology
|April 5, 2011
PubMed
Summary
This summary is machine-generated.

Modern protein sequence comparison methods can detect ancient evolutionary relationships. Combining these with domain analysis aids in predicting protein function and evolution, highlighting the need for standardized benchmarking practices.

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Last Updated: Jun 3, 2026

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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:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Protein sequence comparison methods have advanced significantly, enabling detection of remote homology and ancient evolutionary relationships (up to 3 billion years).
  • Molecular functions and protein domain structures are often conserved over longer evolutionary periods than cellular functions.
  • Remote homology detection, coupled with a domain-centered approach, offers substantial potential for understanding protein function and evolution.

Purpose of the Study:

  • To highlight the potential of modern remote homology detection methods for protein function and evolution elucidation.
  • To address the challenges in comparing existing benchmarking methods due to lack of standardization.
  • To propose a set of guidelines for good-practice benchmarking in this field.

Main Methods:

  • Review and synthesis of recent advances in protein sequence comparison, including nonlinear scoring functions and sequence context information.
  • Evaluation of new software packages for remote homology detection.
  • Development of 10 rules for standardized and reproducible benchmarking.

Main Results:

  • Modern methods, incorporating advanced features and software, show increased sensitivity in detecting distant protein relationships.
  • Domain-centered analysis combined with sensitive sequence comparison is a powerful, yet underexploited, tool.
  • Existing benchmarks are difficult to compare, hindering objective assessment of method performance.

Conclusions:

  • Remote homology detection is crucial for inferring protein function and evolutionary history.
  • Standardized benchmarking is essential for reliable assessment and advancement of these methods.
  • The proposed 10 rules provide a framework for robust and comparable evaluation of protein sequence analysis tools.