Improving position-specific predictions of protein functional sites using phylogenetic motifs

Improving position-specific predictions of protein functional sites using phylogenetic motifs

MOTIVATION Accurate computational prediction of protein functional sites is critical to maximizing the utility of recent high-throughput sequencing efforts. Among the available approaches, position-specific conservation scores remain among the most popular due to their accuracy and ease of computation. Unfortunately, high false positive rates remain a limiting factor. Using phylogenetic motifs ...

Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix

Improving protein structure prediction using multiple sequence-based contact predictions.

Although residue-residue contact maps dictate the topology of proteins, sequence-based ab initio contact predictions have been found little use in actual structure prediction due to the low accuracy. We developed a composite set of nine SVM-based contact predictors that are used in I-TASSER simulation in combination with sparse template contact restraints. When testing the strategy on 273 nonho...

Improving Computational Predictions of Cis- Regulatory Binding Sites

The location of cis-regulatory binding sites determine the connectivity of genetic regulatory networks and therefore constitute a natural focal point for research into the many biological systems controlled by such regulatory networks. Accurate computational prediction of these binding sites would facilitate research into a multitude of key areas, including embryonic development, evolution, pha...

Transcription Factor Binding Sites: Position-Specific and Position-Dependent Modeling

Transcription of a gene is cued by the binding of a protein to a binding site. Transcription factors bind to specific binding sites (TFBSs), of which there may be many for a single transcription factor (1). However, these TFBSs often exhibit a considerable amount of variability, as the sequences consist of similar nucleotides rather than complete replicas of a TFBS (1). The ability to model the...