Strategies for protein structure model generation

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

Abstract

This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling techniques are treated, and how resulting structural models may be selected and refined. We give a concrete flowchart for how to de- cide which modelling strategy is best suited in particular circumstances, and which steps need to be taken in each strategy. Notably, the ability to locate a suitable structural template by homology or fold recognition is crucial; without this models will be of low quality at best. With a template avail- able, the quality of the query-template alignment crucially determines the model quality. We also discuss how other, courser, experimental data may be incorporated in the modelling process to alleviate the problem of missing template structures. Finally, we discuss measures to predict the quality of models generated.
Original languageEnglish
Title of host publicationIntroduction to Structural Bioinformatics
Publication statusSubmitted - 1 Dec 2017

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Model structures
Proteins
Concretes

Keywords

  • q-bio.BM

Cite this

Abeln, S., Heringa, J., & Feenstra, K. A. (2017). Strategies for protein structure model generation. Manuscript submitted for publication. In Introduction to Structural Bioinformatics
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Strategies for protein structure model generation. / 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 deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling techniques are treated, and how resulting structural models may be selected and refined. We give a concrete flowchart for how to de- cide which modelling strategy is best suited in particular circumstances, and which steps need to be taken in each strategy. Notably, the ability to locate a suitable structural template by homology or fold recognition is crucial; without this models will be of low quality at best. With a template avail- able, the quality of the query-template alignment crucially determines the model quality. We also discuss how other, courser, experimental data may be incorporated in the modelling process to alleviate the problem of missing template structures. Finally, we discuss measures to predict the quality of models generated.

AB - This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling techniques are treated, and how resulting structural models may be selected and refined. We give a concrete flowchart for how to de- cide which modelling strategy is best suited in particular circumstances, and which steps need to be taken in each strategy. Notably, the ability to locate a suitable structural template by homology or fold recognition is crucial; without this models will be of low quality at best. With a template avail- able, the quality of the query-template alignment crucially determines the model quality. We also discuss how other, courser, experimental data may be incorporated in the modelling process to alleviate the problem of missing template structures. Finally, we discuss measures to predict the quality of models generated.

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M3 - Chapter

BT - Introduction to Structural Bioinformatics

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Abeln S, Heringa J, Feenstra KA. Strategies for protein structure model generation. In Introduction to Structural Bioinformatics. 2017