SDM : a server for predicting effects of mutations on protein stability
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research..
Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2017 |
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| Erschienen: |
2017 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:45 |
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| Enthalten in: |
Nucleic acids research - 45(2017), W1 vom: 03. Juli, Seite W229-W235 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Pandurangan, Arun Prasad [VerfasserIn] |
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| Links: |
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| Themen: |
Journal Article |
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| Anmerkungen: |
Date Completed 13.06.2019 Date Revised 29.01.2022 published: Print Citation Status MEDLINE |
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| doi: |
10.1093/nar/gkx439 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM272078646 |
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| 500 | |a Date Revised 29.01.2022 | ||
| 500 | |a published: Print | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. | ||
| 520 | |a Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Validation Study | |
| 700 | 1 | |a Ochoa-Montaño, Bernardo |e verfasserin |4 aut | |
| 700 | 1 | |a Ascher, David B |e verfasserin |4 aut | |
| 700 | 1 | |a Blundell, Tom L |e verfasserin |4 aut | |
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