|Search Options||Explanation of Output Data|
|Selection of Long Coiled-Coil Proteins||Release History and Updates|
|Prediction Programs Used||Arabidopsis Database User Survey|
The ARABI-COIL search form provides several search options to identify coiled-coil proteins of interest for the user:
Length of Sequence
Length of Coiled-Coil Domain
This feature allows the user to pre-select a certain coiled-coil domain structure, e.g. N-terminal or C-terminal coiled-coil domains.
Number of Transmembrane Domains
The details page for each protein entry provides the user with the following information about the protein:
Coiled-Coil Prediction Data
Predictions for the following localizations are included in the Arabi-Coil database:
All probability scores for targeting predictions are in the range of 0 (low probability) to 1 (high probability). Scores for ChloroP (0.4 - 0.6 range in raw output) were adjusted to 0 -1 range for better comparability. Hits in the PredictNLS database were given a score of 1.
Results above cut-off values for two confidence levels of scores at 0.5 (low confidence) and 0.75 (high confidence) are marked in yellow and red, respectively.
The following programs and prediction servers were used to generate data for the Arabi-Coil Database.
MultiCoil - prediction of
two- and three-stranded coiled-coils
Wolf, E., Kim, P.S., and Berger, B. (1997): MultiCoil: A Program for Predicting Two- and Three-Stranded Coiled Coils. Protein Sci. 6: 1179-1189.
Center for Biological Sequence
Analysis Prediction Servers
ChloroP 1.1 - prediction of chloroplast
Emanuelsson, O., Nielsen, H., and von Heijne, G. (1999): ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978-984.
SignalP V2.0 - prediction of signal
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997): A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural. Syst. 8: 581-599.
Hidden Markov Model:
Nielsen, H., and Krogh, A. (1998): Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6: 122-130.
TargetP v1.01 - prediction of subcellular
Emanuelsson, O., Nielsen, H., Brunak, S., and von Heijne, G. (2000): Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300: 1005-1016.
TMHMM (v. 2.0) - prediction of transmembrane
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L. (2001): Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305: 567-580.
Other Prediction Servers
HMMTOP - prediction of transmembrane
helices and topology
Tusnády, G.E., and Simon, I. (1998): Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. J. Mol. Biol. 283: 489-506.
MITOPROT - prediction of mitochondrial
Claros, M.G., and Vincens, P (1996). Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241: 779-786.
Predotar - prediction of mitochondrial
and plastid targeting sequences
PredictNLS server - prediction of
nuclear localization signals
Cokol, M., Nair, R., and Rost, B. (2000): Finding Nuclear localization signals. EMBO Rep. 1: 411-415.
PSORT - prediction of protein sorting
signals and localization
Nakai, K., and Horton, P. (1999): PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-35.
version 1.0 - released Nov. 04, 2003
Annkatrin Rose, Sankaraganesh Manikantan, Shannon J. Schraegle, Michael A. Maloy, Eric A. Stahlberg, and Iris Meier (2004). Genome-wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database. Plant Physiol. 134, 927-939. - Abstract at NCBI PubMed
A.R., I.M. (corresponding author): Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA
S.M., S.J.S. (webmaster), M.A.M., E.A.S.: Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, OH 43212, USA
The ARABI-COIL database was made possible with support from the National Science Foundation Project 2010 and the Ohio Supercomputer Center.