Introduction to Protein Structure Prediction

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Abstract

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated.
Original languageEnglish
Title of host publicationIntroduction to Structural Bioinformatics
Publication statusSubmitted - 1 Dec 2017

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Proteins

Keywords

  • q-bio.BM

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Abeln, S., Heringa, J., & Feenstra, K. A. (2017). Introduction to Protein Structure Prediction. Manuscript submitted for publication. In Introduction to Structural Bioinformatics
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Abeln, S, Heringa, J & Feenstra, KA 2017, Introduction to Protein Structure Prediction. in Introduction to Structural Bioinformatics.

Introduction to Protein Structure Prediction. / Abeln, Sanne; Heringa, Jaap; Feenstra, K. Anton.

Introduction to Structural Bioinformatics. 2017.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

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N2 - This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated.

AB - This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated.

KW - q-bio.BM

UR - https://arxiv.org/abs/1712.00407

M3 - Chapter

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Abeln S, Heringa J, Feenstra KA. Introduction to Protein Structure Prediction. In Introduction to Structural Bioinformatics. 2017