DMAPS: a database of multiple alignments for protein structures

The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein structure families in the Protein Data Bank (PDB). Protein structure families have been obtained from four distinct classification methods including SCOP, CATH, ENZYME and CE, and multiple structure alignments have been built for all families containing at least three members, using CE-MC software. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. A web-based query system has been developed to retrieve multiple alignments for these families using the PDB chain ID of any member of a family. Multiple alignments can be viewed or downloaded in six different formats, including JOY/html, TEXT, FASTA, PDB (superimposed coordinates), JOY/postscript and JOY/rtf. DMAPS is accessible online at

STRUCTURE COMPARISON AND ALIGNMENT

Not availabl

WPDB - PC Windows based interrogation of

WPDB version 2.0 is a Microsoft Windows based program for browsing and interrogating native and derived structural features of biological macromolecules using data obtained from the Protein Data Bank (PDB). Major features of WPDB are a 20-fold compression of PDB files and query and analysis tools. The latter permit the geometric and sequence properties of structures to be analyzed individually or through comparative analysis. The object oriented software design provides a high level of interaction between display windows which facilitates information discovery. Three examples are given to illustrate the capabilities of the software, namely: finding the distribution of the most hydrophobic residues in the acid proteases; exploring the geometric features of a 4-helix bundle motif; and examining the effect of antibody binding by comparison of a neuraminidase with a neuraminidase-antibody complex. Additional details are available to World Wide Web (WWW) users at the URL http://cuhhca.hhmi.columbia.edu/wpdb.html