Abstract
In this chapter, we first discuss protein localization in bacteria and evaluate some localization prediction tools on an independent dataset. Next, we focus on β-barrel outer membrane proteins (BOMPs), describing and evaluating new tools for BOMP detection and topology prediction. Finally, we apply general protein structure prediction methods on these proteins to show that the structure of most BOMPs in E. coli can be modeled reliably.
| Original language | English |
|---|---|
| Title of host publication | Data Mining for Systems Biology |
| Subtitle of host publication | Methods and Protocols |
| Editors | Hiroshi Mamitsuka, Minoru Kanehisa, Charles DeLisi |
| Pages | 115-140 |
| Number of pages | 26 |
| DOIs | |
| Publication status | Published - 2013 Jan 8 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 939 |
| ISSN (Print) | 1064-3745 |
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All Science Journal Classification (ASJC) codes
- Molecular Biology
- Genetics
Cite this
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Localization prediction and structure-based in silico analysis of bacterial proteins : With emphasis on outer membrane proteins. / Imai, Kenichiro; Hayat, Sikander; Sakiyama, Noriyuki; Fujita, Naoya; Tomii, Kentaro; Elofsson, Arne; Paul, Brice Horton Ii.
Data Mining for Systems Biology: Methods and Protocols. ed. / Hiroshi Mamitsuka; Minoru Kanehisa; Charles DeLisi. 2013. p. 115-140 (Methods in Molecular Biology; Vol. 939).Research output: Chapter in Book/Report/Conference proceeding › Chapter
TY - CHAP
T1 - Localization prediction and structure-based in silico analysis of bacterial proteins
T2 - With emphasis on outer membrane proteins
AU - Imai, Kenichiro
AU - Hayat, Sikander
AU - Sakiyama, Noriyuki
AU - Fujita, Naoya
AU - Tomii, Kentaro
AU - Elofsson, Arne
AU - Paul, Brice Horton Ii
PY - 2013/1/8
Y1 - 2013/1/8
N2 - In this chapter, we first discuss protein localization in bacteria and evaluate some localization prediction tools on an independent dataset. Next, we focus on β-barrel outer membrane proteins (BOMPs), describing and evaluating new tools for BOMP detection and topology prediction. Finally, we apply general protein structure prediction methods on these proteins to show that the structure of most BOMPs in E. coli can be modeled reliably.
AB - In this chapter, we first discuss protein localization in bacteria and evaluate some localization prediction tools on an independent dataset. Next, we focus on β-barrel outer membrane proteins (BOMPs), describing and evaluating new tools for BOMP detection and topology prediction. Finally, we apply general protein structure prediction methods on these proteins to show that the structure of most BOMPs in E. coli can be modeled reliably.
UR - http://www.scopus.com/inward/record.url?scp=84871900030&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84871900030&partnerID=8YFLogxK
U2 - 10.1007/978-1-62703-107-3-10
DO - 10.1007/978-1-62703-107-3-10
M3 - Chapter
C2 - 23192545
AN - SCOPUS:84871900030
SN - 9781627031066
T3 - Methods in Molecular Biology
SP - 115
EP - 140
BT - Data Mining for Systems Biology
A2 - Mamitsuka, Hiroshi
A2 - Kanehisa, Minoru
A2 - DeLisi, Charles
ER -