We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgrap...
Complex networks have been used successfully in scientific disciplines ranging from sociology to microbiology to describe systems of interacting units. Until recently, studies of...
Protein-protein interactions play a central role in many cellular functions, and as whole-genome data accumulates, computational methods for predicting these interactions become i...
Three strategies are presented for developing a knowledge-based statistical contact potential from computationally hydrated proteins that may be useful in studies of protein foldi...
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the p...