The 2006 Automated Function Prediction Meeting
Citation:
BMC Bioinformatics
2007
8(Suppl 4):S1
Volume 8 Supplement 4
The Second Automated Function Prediction Meeting
Proceedings
Edited by Ana PC Rodrigues, Barry J Grant, Adam Godzik and Iddo Friedberg
The Second Automated Function Prediction Meeting. Go to conference site.
La Jolla, CA, USA30 August - 1 September 2006
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SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, cal...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S2 -
CORRIE: enzyme sequence annotation with confidence estimates
Using a previously developed automated method for enzyme annotation, we report the re-annotation of the ENZYME database and the analysis of local error rates per class. In control experiments, we demonstrate t...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S3 -
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited b...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S4 -
Using structural motif descriptors for sequence-based binding site prediction
Many protein sequences are still poorly annotated. Functional characterization of a protein is often improved by the identification of its interaction partners. Here, we aim to predict protein-protein interact...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S5 -
Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages
Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be ea...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S6 -
An improved method for identifying functionally linked proteins using phylogenetic profiles
Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various ex...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S7 -
Using indirect protein interactions for the prediction of Gene Ontology functions
Protein-protein interaction has been used to complement traditional sequence homology to elucidate protein function. Most existing approaches only make use of direct interactions to infer function, and some ha...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S8 -
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will lead to improved methods for protein-ligand...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S9 -
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
Structural genomics initiatives are producing increasing numbers of three-dimensional (3D) structures for which there is little functional information. Structure-based annotation of molecular function is there...
Citation: BMC Bioinformatics 2007 8(Suppl 4):S10
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