Pspace: a program that assesses protein space

Mihaly Mezei and Ming-Ming Zhou

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, One Gustave L. Levy Place, New York, New York 10029, USA

author email corresponding author email

Source Code for Biology and Medicine 2007, 2:6doi:10.1186/1751-0473-2-6


Published:	23 October 2007

Abstract

Background

We describe a computer program named Pspace designed to a) obtain a reliable basis for the description of three-dimensional structures of a given protein family using homology modeling through selection of an optimal subset of the protein family whose structure would be determined experimentally; and b) aid in the search of orthologs by matching two sets of sequences in three different ways.

Methods

The prioritization is established dynamically as new sequences and new structures are becoming available through ranking proteins by their value in providing structural information about the rest of the family set. The matching can give a list of potential orthologs or it can deduce an overall optimal matching of two sets of sequences.

Results

The various covering strategies and ortholog searches are tested on the bromodomain family.

Conclusion

The possibility of extending this approach to the space of all proteins is discussed.