The Structure-Function Linkage Database
The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Oxford University Press
2013
|
| Online Access: | http://hdl.handle.net/1721.1/83237 https://orcid.org/0000-0003-1045-2660 |
| _version_ | 1811097269118697472 |
|---|---|
| author | Hicks, Michael A. Akiva, Eyal Brown, Shoshana Almonacid, Daniel E. Barber, Alan E., 2nd Custer, Ashley F. Huang, Conrad C. Lauck, Florian Mashiyama, Susan T. Meng, Elaine C. Mischel, David Morris, John H. Ojha, Sunil Schnoes, Alexandra M. Stryke, Doug Yunes, Jeffrey M. Ferrin, Thomas E. Holliday, Gemma L. Babbitt, Patricia C. |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Hicks, Michael A. Akiva, Eyal Brown, Shoshana Almonacid, Daniel E. Barber, Alan E., 2nd Custer, Ashley F. Huang, Conrad C. Lauck, Florian Mashiyama, Susan T. Meng, Elaine C. Mischel, David Morris, John H. Ojha, Sunil Schnoes, Alexandra M. Stryke, Doug Yunes, Jeffrey M. Ferrin, Thomas E. Holliday, Gemma L. Babbitt, Patricia C. |
| author_sort | Hicks, Michael A. |
| collection | MIT |
| description | The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. |
| first_indexed | 2024-09-23T16:56:57Z |
| format | Article |
| id | mit-1721.1/83237 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:56:57Z |
| publishDate | 2013 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/832372022-10-03T09:20:36Z The Structure-Function Linkage Database Hicks, Michael A. Akiva, Eyal Brown, Shoshana Almonacid, Daniel E. Barber, Alan E., 2nd Custer, Ashley F. Huang, Conrad C. Lauck, Florian Mashiyama, Susan T. Meng, Elaine C. Mischel, David Morris, John H. Ojha, Sunil Schnoes, Alexandra M. Stryke, Doug Yunes, Jeffrey M. Ferrin, Thomas E. Holliday, Gemma L. Babbitt, Patricia C. Massachusetts Institute of Technology. Department of Chemical Engineering Hicks, Michael A. The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. 2013-12-23T19:09:29Z 2013-12-23T19:09:29Z 2013-11 2013-10 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/83237 Akiva, E., S. Brown, D. E. Almonacid, A. E. Barber, A. F. Custer, M. A. Hicks, C. C. Huang, et al. “The Structure-Function Linkage Database.” Nucleic Acids Research (November 23, 2013). https://orcid.org/0000-0003-1045-2660 en_US http://dx.doi.org/10.1093/nar/gkt1130 Nucleic Acids Research http://creativecommons.org/licenses/by/3.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Hicks, Michael A. Akiva, Eyal Brown, Shoshana Almonacid, Daniel E. Barber, Alan E., 2nd Custer, Ashley F. Huang, Conrad C. Lauck, Florian Mashiyama, Susan T. Meng, Elaine C. Mischel, David Morris, John H. Ojha, Sunil Schnoes, Alexandra M. Stryke, Doug Yunes, Jeffrey M. Ferrin, Thomas E. Holliday, Gemma L. Babbitt, Patricia C. The Structure-Function Linkage Database |
| title | The Structure-Function Linkage Database |
| title_full | The Structure-Function Linkage Database |
| title_fullStr | The Structure-Function Linkage Database |
| title_full_unstemmed | The Structure-Function Linkage Database |
| title_short | The Structure-Function Linkage Database |
| title_sort | structure function linkage database |
| url | http://hdl.handle.net/1721.1/83237 https://orcid.org/0000-0003-1045-2660 |
| work_keys_str_mv | AT hicksmichaela thestructurefunctionlinkagedatabase AT akivaeyal thestructurefunctionlinkagedatabase AT brownshoshana thestructurefunctionlinkagedatabase AT almonaciddaniele thestructurefunctionlinkagedatabase AT barberalane2nd thestructurefunctionlinkagedatabase AT custerashleyf thestructurefunctionlinkagedatabase AT huangconradc thestructurefunctionlinkagedatabase AT lauckflorian thestructurefunctionlinkagedatabase AT mashiyamasusant thestructurefunctionlinkagedatabase AT mengelainec thestructurefunctionlinkagedatabase AT mischeldavid thestructurefunctionlinkagedatabase AT morrisjohnh thestructurefunctionlinkagedatabase AT ojhasunil thestructurefunctionlinkagedatabase AT schnoesalexandram thestructurefunctionlinkagedatabase AT strykedoug thestructurefunctionlinkagedatabase AT yunesjeffreym thestructurefunctionlinkagedatabase AT ferrinthomase thestructurefunctionlinkagedatabase AT hollidaygemmal thestructurefunctionlinkagedatabase AT babbittpatriciac thestructurefunctionlinkagedatabase AT hicksmichaela structurefunctionlinkagedatabase AT akivaeyal structurefunctionlinkagedatabase AT brownshoshana structurefunctionlinkagedatabase AT almonaciddaniele structurefunctionlinkagedatabase AT barberalane2nd structurefunctionlinkagedatabase AT custerashleyf structurefunctionlinkagedatabase AT huangconradc structurefunctionlinkagedatabase AT lauckflorian structurefunctionlinkagedatabase AT mashiyamasusant structurefunctionlinkagedatabase AT mengelainec structurefunctionlinkagedatabase AT mischeldavid structurefunctionlinkagedatabase AT morrisjohnh structurefunctionlinkagedatabase AT ojhasunil structurefunctionlinkagedatabase AT schnoesalexandram structurefunctionlinkagedatabase AT strykedoug structurefunctionlinkagedatabase AT yunesjeffreym structurefunctionlinkagedatabase AT ferrinthomase structurefunctionlinkagedatabase AT hollidaygemmal structurefunctionlinkagedatabase AT babbittpatriciac structurefunctionlinkagedatabase |