Recent studies in protein sequence analysis have leveraged the power of unlabeled data. For example, the profile and mismatch neighborhood kernels have shown significant improveme...
Background: The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evoluti...
MALISAM (manual alignments for structurally analogous motifs) represents the first database containing pairs of structural analogs and their alignments. To find reliable analogs, ...
PSI-BLAST remains one of the popular tools for searching remote homologs in sequence databases. We recently demonstrated that hybrid alignment can function as the alignment core f...
Background: Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represent...