Читать книгу Biological Language Model - Qiwen Dong - Страница 9

Contents

East China Normal University Scientific Reports

Preface

Acknowledgments

1.Introduction

1.1Background and Motivation

1.2Related Topics

1.3Organization of the Book Content

References

2.Linguistic Feature Analysis of Protein Sequences

2.1Motivation and Basic Idea

2.2Comparative n-gram Analysis

2.3The Zipf Law Analysis

2.4Distinguishing the Organisms by Uni-Gram Model

2.5Conclusions

References

3.Amino Acid Encoding for Protein Sequence

3.1Motivation and Basic Idea

3.2Related Work

3.3Discussion

3.4The Assessment of Encoding Methods for Protein Secondary Structure Prediction

3.5Assessments of Encoding Methods for Protein Fold Recognition

3.6Conclusions

References

4.Remote Homology Detection

4.1Motivation and Basic Idea

4.2Related Work

4.3Latent Semantic Analysis

4.4Auto-cross Covariance Transformation

4.5Conclusions

References

5.Structure Prediction

5.1Motivation and Basic Idea

5.2Related Work

5.3Domain Boundary Prediction

5.4Building Blocks of Protein Local Structure

5.5Characterization of Protein Flexibility Based on Structural Alphabets

5.6Novel Nonlinear Knowledge-based Mean Force Potentials

5.7Conclusions

References

6.Function Prediction

6.1Motivation and Basic Idea

6.2Profile-level Interface Propensities for Binding Site Prediction

6.3Gene Ontology-Based Protein Function Prediction

6.4Prediction of Protein–Protein Interaction from Primary Sequences

6.5Identifying the Missing Proteins using the Biological Language Model

6.6Conclusions

References

7.Summary and Future Perspectives

Index