The Experts below are selected from a list of 9270 Experts worldwide ranked by ideXlab platform

Michelle M. Hill - One of the best experts on this subject based on the ideXlab platform.

  • raftprot v2 understanding membrane microdomain function through lipid raft proteomes
    Nucleic Acids Research, 2019
    Co-Authors: Michelle M. Hill, Anup Shah, Ahmed Mohamed, David Chen
    Abstract:

    Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contaminant proteins. To enable integrated analyses, we previously developed RaftProt (http://lipid-raft-Database.di.uq.edu.au/), a Searchable Database of mammalian lipid raft-associated proteins. Despite being a highly used resource, further developments in annotation and utilities were required. Here, we present RaftProt V2 (http://raftprot.org), an improved update of RaftProt. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have implemented a stringent annotation based on experimental evidence level to assist in identification of possible contaminant proteins. RaftProt V2 allows for simultaneous search of multiple proteins/experiments at the cell/tissue type and UniRef/Gene level, where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed to enable interactive data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function through integrative analysis of datasets collected from diverse tissue and conditions. Database URL: http://raftprot.org.

  • RaftProt: mammalian lipid raft proteome Database.
    Nucleic acids research, 2014
    Co-Authors: Anup Shah, David Chen, Akash R Boda, Leonard J Foster, Melissa J Davis, Michelle M. Hill
    Abstract:

    RaftProt (http://lipid-raft-Database.di.uq.edu.au/) is a Database of mammalian lipid raft-associated proteins as reported in high-throughput mass spectrometry studies. Lipid rafts are specialized membrane microdomains enriched in cholesterol and sphingolipids thought to act as dynamic signalling and sorting platforms. Given their fundamental roles in cellular regulation, there is a plethora of information on the size, composition and regulation of these membrane microdomains, including a large number of proteomics studies. To facilitate the mining and analysis of published lipid raft proteomics studies, we have developed a Searchable Database RaftProt. In addition to browsing the studies, performing basic queries by protein and gene names, searching experiments by cell, tissue and organisms; we have implemented several advanced features to facilitate data mining. To address the issue of potential bias due to biochemical preparation procedures used, we have captured the lipid raft preparation methods and implemented advanced search option for methodology and sample treatment conditions, such as cholesterol depletion. Furthermore, we have identified a list of high confidence proteins, and enabled searching only from this list of likely bona fide lipid raft proteins. Given the apparent biological importance of lipid raft and their associated proteins, this Database would constitute a key resource for the scientific community.

Brent M Znosko - One of the best experts on this subject based on the ideXlab platform.

  • rna cossmos 2 0 an improved Searchable Database of secondary structure motifs in rna three dimensional structures
    Database, 2020
    Co-Authors: Katherine E Richardson, Charles C Kirkpatrick, Brent M Znosko
    Abstract:

    The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, Database is a freely accessible online Database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant Database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded Database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure Database; it now has the capability of analyzing, comparing and summarizing search results. Database URL: http://rnacossmos.com.

  • rna cossmos characterization of secondary structure motifs a Searchable Database of secondary structure motifs in rna three dimensional structures
    Nucleic Acids Research, 2012
    Co-Authors: Pamela L Vanegas, Charles C Kirkpatrick, Graham A Hudson, Amber R Davis, Shannon C Kelly, Brent M Znosko
    Abstract:

    RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several Databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) Database is a freely accessible and Searchable online Database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos Database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the Database. False positives were defined, identified and reclassified or omitted from the Database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos Database is automatically updated weekly and is available at http://cossmos.slu.edu.

Ahmed Mohamed - One of the best experts on this subject based on the ideXlab platform.

  • raftprot v2 understanding membrane microdomain function through lipid raft proteomes
    Nucleic Acids Research, 2019
    Co-Authors: Michelle M. Hill, Anup Shah, Ahmed Mohamed, David Chen
    Abstract:

    Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contaminant proteins. To enable integrated analyses, we previously developed RaftProt (http://lipid-raft-Database.di.uq.edu.au/), a Searchable Database of mammalian lipid raft-associated proteins. Despite being a highly used resource, further developments in annotation and utilities were required. Here, we present RaftProt V2 (http://raftprot.org), an improved update of RaftProt. Besides the addition of new datasets and re-mapping of all entries to both UniProt and UniRef IDs, we have implemented a stringent annotation based on experimental evidence level to assist in identification of possible contaminant proteins. RaftProt V2 allows for simultaneous search of multiple proteins/experiments at the cell/tissue type and UniRef/Gene level, where correlations, interactions or overlaps can be investigated. The web-interface has been completely re-designed to enable interactive data and subset selection, correlation analysis and network visualization. Overall, RaftProt aims to advance our understanding of lipid raft function through integrative analysis of datasets collected from diverse tissue and conditions. Database URL: http://raftprot.org.

Pamela L Vanegas - One of the best experts on this subject based on the ideXlab platform.

  • rna cossmos characterization of secondary structure motifs a Searchable Database of secondary structure motifs in rna three dimensional structures
    Nucleic Acids Research, 2012
    Co-Authors: Pamela L Vanegas, Charles C Kirkpatrick, Graham A Hudson, Amber R Davis, Shannon C Kelly, Brent M Znosko
    Abstract:

    RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several Databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) Database is a freely accessible and Searchable online Database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos Database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the Database. False positives were defined, identified and reclassified or omitted from the Database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos Database is automatically updated weekly and is available at http://cossmos.slu.edu.

Charles C Kirkpatrick - One of the best experts on this subject based on the ideXlab platform.

  • rna cossmos 2 0 an improved Searchable Database of secondary structure motifs in rna three dimensional structures
    Database, 2020
    Co-Authors: Katherine E Richardson, Charles C Kirkpatrick, Brent M Znosko
    Abstract:

    The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, Database is a freely accessible online Database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant Database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded Database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure Database; it now has the capability of analyzing, comparing and summarizing search results. Database URL: http://rnacossmos.com.

  • rna cossmos characterization of secondary structure motifs a Searchable Database of secondary structure motifs in rna three dimensional structures
    Nucleic Acids Research, 2012
    Co-Authors: Pamela L Vanegas, Charles C Kirkpatrick, Graham A Hudson, Amber R Davis, Shannon C Kelly, Brent M Znosko
    Abstract:

    RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several Databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) Database is a freely accessible and Searchable online Database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos Database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the Database. False positives were defined, identified and reclassified or omitted from the Database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos Database is automatically updated weekly and is available at http://cossmos.slu.edu.