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SDM—a server for predicting effects of mutations on protein stability and malfunction
The sheer volume of non-synonymous single nucleotide polymorphisms that have been generated in recent years from projects such as the Human Genome Project, the HapMap Project and Genome-Wide Association Studies means that it is not possible to characterize all mutations experimentally on the gene pr...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125769/ https://www.ncbi.nlm.nih.gov/pubmed/21593128 http://dx.doi.org/10.1093/nar/gkr363 |
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author | Worth, Catherine L. Preissner, Robert Blundell, Tom L. |
author_facet | Worth, Catherine L. Preissner, Robert Blundell, Tom L. |
author_sort | Worth, Catherine L. |
collection | PubMed |
description | The sheer volume of non-synonymous single nucleotide polymorphisms that have been generated in recent years from projects such as the Human Genome Project, the HapMap Project and Genome-Wide Association Studies means that it is not possible to characterize all mutations experimentally on the gene products, i.e. elucidate the effects of mutations on protein structure and function. However, automatic methods that can predict the effects of mutations will allow a reduced set of mutations to be studied. Site Directed Mutator (SDM) is a statistical potential energy function that uses environment-specific amino-acid substitution frequencies within homologous protein families to calculate a stability score, which is analogous to the free energy difference between the wild-type and mutant protein. Here, we present a web server for SDM (http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php), which has obtained more than 10 000 submissions since being online in April 2008. To run SDM, users must upload a wild-type structure and the position and amino acid type of the mutation. The results returned include information about the local structural environment of the wild-type and mutant residues, a stability score prediction and prediction of disease association. Additionally, the wild-type and mutant structures are displayed in a Jmol applet with the relevant residues highlighted. |
format | Online Article Text |
id | pubmed-3125769 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257692011-07-05 SDM—a server for predicting effects of mutations on protein stability and malfunction Worth, Catherine L. Preissner, Robert Blundell, Tom L. Nucleic Acids Res Articles The sheer volume of non-synonymous single nucleotide polymorphisms that have been generated in recent years from projects such as the Human Genome Project, the HapMap Project and Genome-Wide Association Studies means that it is not possible to characterize all mutations experimentally on the gene products, i.e. elucidate the effects of mutations on protein structure and function. However, automatic methods that can predict the effects of mutations will allow a reduced set of mutations to be studied. Site Directed Mutator (SDM) is a statistical potential energy function that uses environment-specific amino-acid substitution frequencies within homologous protein families to calculate a stability score, which is analogous to the free energy difference between the wild-type and mutant protein. Here, we present a web server for SDM (http://www-cryst.bioc.cam.ac.uk/~sdm/sdm.php), which has obtained more than 10 000 submissions since being online in April 2008. To run SDM, users must upload a wild-type structure and the position and amino acid type of the mutation. The results returned include information about the local structural environment of the wild-type and mutant residues, a stability score prediction and prediction of disease association. Additionally, the wild-type and mutant structures are displayed in a Jmol applet with the relevant residues highlighted. Oxford University Press 2011-07-01 2011-05-18 /pmc/articles/PMC3125769/ /pubmed/21593128 http://dx.doi.org/10.1093/nar/gkr363 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Worth, Catherine L. Preissner, Robert Blundell, Tom L. SDM—a server for predicting effects of mutations on protein stability and malfunction |
title | SDM—a server for predicting effects of mutations on protein stability and malfunction |
title_full | SDM—a server for predicting effects of mutations on protein stability and malfunction |
title_fullStr | SDM—a server for predicting effects of mutations on protein stability and malfunction |
title_full_unstemmed | SDM—a server for predicting effects of mutations on protein stability and malfunction |
title_short | SDM—a server for predicting effects of mutations on protein stability and malfunction |
title_sort | sdm—a server for predicting effects of mutations on protein stability and malfunction |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125769/ https://www.ncbi.nlm.nih.gov/pubmed/21593128 http://dx.doi.org/10.1093/nar/gkr363 |
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