ChanFAD: A Functional Annotation Database for Ion Channels
Ion channels are integral membrane protein complexes critical for regulation of membrane potential, cell volume, and other signaling events. As complex molecular assemblies with many interacting partners, ion channels have multiple structural and functional domains. While channel sequence and functi...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-07-01
|
| Series: | Frontiers in Bioinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2022.835805/full |
| _version_ | 1811287807422889984 |
|---|---|
| author | Elizabeth V. Castro Elizabeth V. Castro John W. Shepherd Ryan S. Guggenheim Ryan S. Guggenheim Manimone Sengvoravong Bailey C. Hall McKenzie K. Chappell McKenzie K. Chappell Jessica A. Hearn Jessica A. Hearn Olivia N. Caraccio Cora Bissman Cora Bissman Sydney Lantow Damian Buehner Harry R. Costlow David M. Prather Abigail M. Zonza Mallory Witt Jeffrey A. Zahratka Jeffrey A. Zahratka |
| author_facet | Elizabeth V. Castro Elizabeth V. Castro John W. Shepherd Ryan S. Guggenheim Ryan S. Guggenheim Manimone Sengvoravong Bailey C. Hall McKenzie K. Chappell McKenzie K. Chappell Jessica A. Hearn Jessica A. Hearn Olivia N. Caraccio Cora Bissman Cora Bissman Sydney Lantow Damian Buehner Harry R. Costlow David M. Prather Abigail M. Zonza Mallory Witt Jeffrey A. Zahratka Jeffrey A. Zahratka |
| author_sort | Elizabeth V. Castro |
| collection | DOAJ |
| description | Ion channels are integral membrane protein complexes critical for regulation of membrane potential, cell volume, and other signaling events. As complex molecular assemblies with many interacting partners, ion channels have multiple structural and functional domains. While channel sequence and functional data are readily available across multiple online resources, there is an unmet need for functional annotation directly relating primary sequence information, 2D interactions, and three-dimensional protein structure. To this end, we present ChanFAD (Channel Functional Annotation Database), to provide the research community with a centralized resource for ion channel structure and functional data. ChanFAD provides functional annotation of PDB structures built on the National Center for Biotechnology Information’s iCn3D structure viewing tool while providing additional information such as primary sequence, organism, and relevant links to other databases. Here we provide a brief tour of ChanFAD functionality while showing example use cases involving drug-channel interactions and structural changes based on mutation. ChanFAD is freely available and can be accessed at https://www.chanfad.org/. |
| first_indexed | 2024-04-13T03:26:12Z |
| format | Article |
| id | doaj.art-5bc9a44b001049f9b61703c75d62e4f4 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-04-13T03:26:12Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-5bc9a44b001049f9b61703c75d62e4f42022-12-22T03:04:39ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472022-07-01210.3389/fbinf.2022.835805835805ChanFAD: A Functional Annotation Database for Ion ChannelsElizabeth V. Castro0Elizabeth V. Castro1John W. Shepherd2Ryan S. Guggenheim3Ryan S. Guggenheim4Manimone Sengvoravong5Bailey C. Hall6McKenzie K. Chappell7McKenzie K. Chappell8Jessica A. Hearn9Jessica A. Hearn10Olivia N. Caraccio11Cora Bissman12Cora Bissman13Sydney Lantow14Damian Buehner15Harry R. Costlow16David M. Prather17Abigail M. Zonza18Mallory Witt19Jeffrey A. Zahratka20Jeffrey A. Zahratka21Department of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Psychology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Psychology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Biology and Geology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Biology and Geology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Biology and Geology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Chemistry, Baldwin Wallace University, Berea, OH, United StatesDepartment of Biology and Geology, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Neuroscience, Baldwin Wallace University, Berea, OH, United StatesDepartment of Biology and Geology, Baldwin Wallace University, Berea, OH, United StatesIon channels are integral membrane protein complexes critical for regulation of membrane potential, cell volume, and other signaling events. As complex molecular assemblies with many interacting partners, ion channels have multiple structural and functional domains. While channel sequence and functional data are readily available across multiple online resources, there is an unmet need for functional annotation directly relating primary sequence information, 2D interactions, and three-dimensional protein structure. To this end, we present ChanFAD (Channel Functional Annotation Database), to provide the research community with a centralized resource for ion channel structure and functional data. ChanFAD provides functional annotation of PDB structures built on the National Center for Biotechnology Information’s iCn3D structure viewing tool while providing additional information such as primary sequence, organism, and relevant links to other databases. Here we provide a brief tour of ChanFAD functionality while showing example use cases involving drug-channel interactions and structural changes based on mutation. ChanFAD is freely available and can be accessed at https://www.chanfad.org/.https://www.frontiersin.org/articles/10.3389/fbinf.2022.835805/fullion channelsfunctional annotationprotein structuredatabaseproteomics |
| spellingShingle | Elizabeth V. Castro Elizabeth V. Castro John W. Shepherd Ryan S. Guggenheim Ryan S. Guggenheim Manimone Sengvoravong Bailey C. Hall McKenzie K. Chappell McKenzie K. Chappell Jessica A. Hearn Jessica A. Hearn Olivia N. Caraccio Cora Bissman Cora Bissman Sydney Lantow Damian Buehner Harry R. Costlow David M. Prather Abigail M. Zonza Mallory Witt Jeffrey A. Zahratka Jeffrey A. Zahratka ChanFAD: A Functional Annotation Database for Ion Channels Frontiers in Bioinformatics ion channels functional annotation protein structure database proteomics |
| title | ChanFAD: A Functional Annotation Database for Ion Channels |
| title_full | ChanFAD: A Functional Annotation Database for Ion Channels |
| title_fullStr | ChanFAD: A Functional Annotation Database for Ion Channels |
| title_full_unstemmed | ChanFAD: A Functional Annotation Database for Ion Channels |
| title_short | ChanFAD: A Functional Annotation Database for Ion Channels |
| title_sort | chanfad a functional annotation database for ion channels |
| topic | ion channels functional annotation protein structure database proteomics |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2022.835805/full |
| work_keys_str_mv | AT elizabethvcastro chanfadafunctionalannotationdatabaseforionchannels AT elizabethvcastro chanfadafunctionalannotationdatabaseforionchannels AT johnwshepherd chanfadafunctionalannotationdatabaseforionchannels AT ryansguggenheim chanfadafunctionalannotationdatabaseforionchannels AT ryansguggenheim chanfadafunctionalannotationdatabaseforionchannels AT manimonesengvoravong chanfadafunctionalannotationdatabaseforionchannels AT baileychall chanfadafunctionalannotationdatabaseforionchannels AT mckenziekchappell chanfadafunctionalannotationdatabaseforionchannels AT mckenziekchappell chanfadafunctionalannotationdatabaseforionchannels AT jessicaahearn chanfadafunctionalannotationdatabaseforionchannels AT jessicaahearn chanfadafunctionalannotationdatabaseforionchannels AT oliviancaraccio chanfadafunctionalannotationdatabaseforionchannels AT corabissman chanfadafunctionalannotationdatabaseforionchannels AT corabissman chanfadafunctionalannotationdatabaseforionchannels AT sydneylantow chanfadafunctionalannotationdatabaseforionchannels AT damianbuehner chanfadafunctionalannotationdatabaseforionchannels AT harryrcostlow chanfadafunctionalannotationdatabaseforionchannels AT davidmprather chanfadafunctionalannotationdatabaseforionchannels AT abigailmzonza chanfadafunctionalannotationdatabaseforionchannels AT mallorywitt chanfadafunctionalannotationdatabaseforionchannels AT jeffreyazahratka chanfadafunctionalannotationdatabaseforionchannels AT jeffreyazahratka chanfadafunctionalannotationdatabaseforionchannels |