Volume 14 Supplement 3
Edited by Iddo Friedberg and Predrag Radivojac
The Automated Function Prediction meeting at ISMB 2011 was supported by a US National Institutes of Health grant R13 HG006079-01A1 awarded to PR and a US Department of Energy, Office of Science grant DE-SC0006807TDD awarded to IF. The meeting organizers gratefully acknowledge the ongoing support of the International Society for Computational Biology to the Automated Function Prediction Special Interest Group.
Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations. Go to conference site.
Vienna, Austria15-16 July 2011
Accurate protein function annotation is a severe bottleneck when utilizing the deluge of high-throughput, next generation sequencing data. Keeping database annotations up-to-date has become a major scientific ...
Many Automatic Function Prediction (AFP) methods were developed to cope with an increasing growth of the number of gene sequences that are available from high throughput sequencing experiments. To support the ...
Predicting protein function from sequence is useful for biochemical experiment design, mutagenesis analysis, protein engineering, protein design, biological pathway analysis, drug design, disease diagnosis, an...
In the genomic era a key issue is protein annotation, namely how to endow protein sequences, upon translation from the corresponding genes, with structural and functional features. Routinely this operation is ...
Here we assessed the use of domain families for predicting the functions of whole proteins. These 'functional families' (FunFams) were derived using a protocol that combines sequence clustering with supervised...
Annotating protein function with both high accuracy and sensitivity remains a major challenge in structural genomics. One proven computational strategy has been to group a few key functional amino acids into t...
Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference.
Protein function determination is a key challenge in the post-genomic era. Experimental determination of protein functions is accurate, but time-consuming and resource-intensive. A cost-effective alternative i...
Computational/manual annotations of protein functions are one of the first routes to making sense of a newly sequenced genome. Protein domain predictions form an essential part of this annotation process. This...
Combining heterogeneous sources of data is essential for accurate prediction of protein function. The task is complicated by the fact that while sequence-based features can be readily compared across species, ...
Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping ...
Predicting the function of newly sequenced proteins is crucial due to the pace at which these raw sequences are being obtained. Almost all resources for predicting protein function assign functional terms to w...
The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and...
Advances in sequencing technology over the past decade have resulted in an abundance of sequenced proteins whose function is yet unknown. As such, computational systems that can automatically predict and annot...
The assignment of gene function remains a difficult but important task in computational biology. The establishment of the first Critical Assessment of Functional Annotation (CAFA) was aimed at increasing progr...
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