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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Deep learning for protein complex structure prediction.

Patrick Bryant¹

¹Science for Life Laboratory, 172 21 Solna, Sweden; Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.

Current Opinion in Structural Biology

|February 2, 2023

Summary

Advanced protein complex structure prediction now rivals experimental accuracy for dimers. Challenges remain in predicting protein disorder and host-pathogen interactions, requiring further research.

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Published on: July 16, 2017

Area of Science:

Structural biology
Computational biology
Biochemistry

Background:

Recent advancements in protein complex structure prediction have achieved high accuracy, comparable to experimental methods for certain complexes.
This accuracy is predominantly seen in predicting dimeric protein complexes.

Purpose of the Study:

To review the foundational methods enabling accurate protein complex structure prediction.
To identify and discuss limitations in current prediction capabilities, including protein disorder and host-pathogen interactions.
To propose future directions for addressing these remaining challenges.

Main Methods:

Review of computational algorithms and machine learning models for protein structure prediction.
Analysis of datasets and benchmarks for evaluating prediction accuracy.
Comparative assessment of prediction methods against experimental data.

Main Results:

Current methods demonstrate high accuracy for predicting the structure of dimeric protein complexes.
Significant challenges persist in accurately predicting protein disorder within complexes.
Predicting the structural basis of host-pathogen interactions remains a complex problem.

Conclusions:

The field has made substantial progress in protein complex structure prediction, particularly for dimers.
Further methodological development is needed to address protein disorder and host-pathogen interactions.
Future research should focus on enhancing predictive power for more complex biological systems.