Learn More
MOTIVATION Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are(More)
MOTIVATION All residues in a protein are not equally important. Some are essential for the proper structure and function of the protein, whereas others can be readily replaced. Conservation analysis is one of the most widely used methods for predicting these functionally important residues in protein sequences. RESULTS We introduce an(More)
MOTIVATION Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optimized. It is NP-complete to find even a reasonable approximate solution to this problem. We seek to put(More)
MOTIVATION Clustering algorithms play an important role in the analysis of biological networks, and can be used to uncover functional modules and obtain hints about cellular organization. While most available clustering algorithms work well on biological networks of moderate size, such as the yeast protein physical interaction network, they either fail or(More)
Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based(More)
In a broad range of organisms, Piwi-interacting RNAs (piRNAs) have emerged as core components of a surveillance system that protects the genome by silencing transposable and repetitive elements. A vast proportion of piRNAs is produced from discrete genomic loci, termed piRNA clusters, which are generally embedded in heterochromatic regions. The molecular(More)
MOTIVATION Within a homologous protein family, proteins may be grouped into subtypes that share specific functions that are not common to the entire family. Often, the amino acids present in a small number of sequence positions determine each protein's particular functional specificity. Knowledge of these specificity determining positions (SDPs) aids in(More)