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How do I get the most out of my protein sequence using bioinformatics tools?
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an unch...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8411974/ https://www.ncbi.nlm.nih.gov/pubmed/34473083 http://dx.doi.org/10.1107/S2059798321007907 |
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author | Pereira, Joana Alva, Vikram |
author_facet | Pereira, Joana Alva, Vikram |
author_sort | Pereira, Joana |
collection | PubMed |
description | Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on. |
format | Online Article Text |
id | pubmed-8411974 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-84119742021-09-13 How do I get the most out of my protein sequence using bioinformatics tools? Pereira, Joana Alva, Vikram Acta Crystallogr D Struct Biol Ccp4 Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on. International Union of Crystallography 2021-08-24 /pmc/articles/PMC8411974/ /pubmed/34473083 http://dx.doi.org/10.1107/S2059798321007907 Text en © Pereira and Alva 2021 https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Ccp4 Pereira, Joana Alva, Vikram How do I get the most out of my protein sequence using bioinformatics tools? |
title | How do I get the most out of my protein sequence using bioinformatics tools? |
title_full | How do I get the most out of my protein sequence using bioinformatics tools? |
title_fullStr | How do I get the most out of my protein sequence using bioinformatics tools? |
title_full_unstemmed | How do I get the most out of my protein sequence using bioinformatics tools? |
title_short | How do I get the most out of my protein sequence using bioinformatics tools? |
title_sort | how do i get the most out of my protein sequence using bioinformatics tools? |
topic | Ccp4 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8411974/ https://www.ncbi.nlm.nih.gov/pubmed/34473083 http://dx.doi.org/10.1107/S2059798321007907 |
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