Collection Citation
| Collection Title | DAPS: Database of Aligned Protein Structures | ||
| Collection Creator/PI | Mallick, Parag; Rice, Danny; Eisenberg, David | ||
| Collection Sponsor | USDOE - Office of Science (SC) | ||
| Host Website | UCLA-DOE Institute for Genomics and Proteomics | ||
| Other Related Organizations | UCLA-DOE Institute for Genomics and Proteomics | ||
| Main Content Type | Specialized Mix | ||
| Subject Categories | 59 - BASIC BIOLOGICAL SCIENCES | ||
| Keywords | Protein structures; Domains; Gaps; Sequence; Fold; Genomics; Bioinformatics | ||
| Description | DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html] | ||
| DDE Number | DDE00363 | ||
| Special Interface | No | ||
| Registration_Required | No |
