Finding sequence motifs in groups of functionally related proteins.

Finding Compact Structural Motifs in Many Proteins

Multiple structural alignment is a fundamental problem in computational biology. Compared with sequence alignment, structural alignment is more powerful in detecting the evolutionary relationship of proteins. A variety of algorithms have been proposed to attack this problem, however, they are either heuristic without theoretical performance guarantee, or inefficient for employing an exhaustive ...

SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context

Recurring local sequence motifs in proteins.

We describe a completely automated approach to identifying local sequence motifs that transcend protein family boundaries. Cluster analysis is used to identify recurring patterns of variation at single positions and in short segments of contiguous positions in multiple sequence alignments for a non-redundant set of protein families. Parallel experiments on simulated data sets constructed with t...

A Method for Automatically Finding Structural Motifs in Proteins

A lot of work has gone into predicting the secondary (small scale) structure of proteins from their amino acid sequence. Current research indicates that there are limits on how well secondary structure can be predicted from local sequence information. To further advance prediction, the interactions between elements of secondary structure which are inherently non-local, have to be better underst...

Phosphatidylinositol transfer proteins: sequence motifs in structural and evolutionary analyses.

Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of inositol and diacylglycerol second messengers, and are found in most metazoan organisms. While PITPs are known to carry out crucial cell-signaling roles in many organisms, the struc...