Abstract
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1019-1037 |
| Number of pages | 19 |
| Journal | Biochimica et Biophysica Acta - Proteins and Proteomics |
| Volume | 1854 |
| Issue number | 8 |
| DOIs | |
| State | Published - Aug 1 2015 |
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Keywords
- Enzyme
- Function discovery
- Protein family
- Protein sequence analysis
- Web tool
ASJC Scopus subject areas
- Analytical Chemistry
- Biophysics
- Biochemistry
- Molecular Biology
Cite this
Enzyme function initiative-enzyme similarity tool (EFI-EST) : A web tool for generating protein sequence similarity networks. / Gerlt, John A.; Bouvier, Jason T.; Davidson, Daniel B.; Imker, Heidi J.; Sadkhin, Boris; Slater, David R.; Whalen, Katie L.
In: Biochimica et Biophysica Acta - Proteins and Proteomics, Vol. 1854, No. 8, 01.08.2015, p. 1019-1037.Research output: Contribution to journal › Review article
}
TY - JOUR
T1 - Enzyme function initiative-enzyme similarity tool (EFI-EST)
T2 - A web tool for generating protein sequence similarity networks
AU - Gerlt, John A.
AU - Bouvier, Jason T.
AU - Davidson, Daniel B.
AU - Imker, Heidi J.
AU - Sadkhin, Boris
AU - Slater, David R.
AU - Whalen, Katie L.
PY - 2015/8/1
Y1 - 2015/8/1
N2 - The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
AB - The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
KW - Enzyme
KW - Function discovery
KW - Protein family
KW - Protein sequence analysis
KW - Web tool
UR - http://www.scopus.com/inward/record.url?scp=84929376894&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84929376894&partnerID=8YFLogxK
U2 - 10.1016/j.bbapap.2015.04.015
DO - 10.1016/j.bbapap.2015.04.015
M3 - Review article
C2 - 25900361
AN - SCOPUS:84929376894
VL - 1854
SP - 1019
EP - 1037
JO - Biochimica et Biophysica Acta - Proteins and Proteomics
JF - Biochimica et Biophysica Acta - Proteins and Proteomics
SN - 1570-9639
IS - 8
ER -