SBASE 8.0 is the eighth release of the SBASE library of protein domain sequences that contains 294 898 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to most major sequence databases and sequence pattern collections. The entries are clustered into over 2005 statistically validated domain groups (SBASE-A) and 595 non-validated groups (SBASE-...

We introduce a novel method for predicting the secondary structure of proteins, PREDICT (PRofile Enumeration DICTionary), in which the nearest-neighbor method is applied to a pattern space. For a given protein sequence, PSI-BLAST is used to generate a profile that defines patterns for amino acid residues and their local sequence environments. By applying the PSI-BLAST to protein sequences with ...

MOTIVATION Many of the most interesting functional and evolutionary relationships among proteins are so ancient that they cannot be reliably detected through sequence analysis and are apparent only through a comparison of the tertiary structures. The conserved features can often be described as structural motifs consisting of a few single residues or Secondary Structure (SS) elements. Confidenc...

background: bone morphogenetic proteins (bmps) belong to the transforming growth factor-β (tgf-β) superfamily, and play an important role in bone metabolism. recombinant forms of bmp-2 and bmp-7 are the only bmps used clinically. in this study the mature part of human bone morphogenetic protein-7 (bmp-7) was engineered through substitution of the bmp-7 n-terminal sequence by heparin-binding sit...

Since the advent of large-scale genomic sequencing, and the consequent availability of large numbers of homologous protein sequences, there has been burgeoning development of methods for extracting functional information from multiple sequence alignments (MSAs). One type of analysis seeks to identify specificity determining positions (SDPs) based on the assumption that such positions are highly...