Database of protein complexes

Database of protein-protein complexes
as of 2006-11-02 (links to older versions of the database are on the bottom of the front page)
P.J.Kundrotas and E.Alexov (2007) Nucleic Acids Research, v.35, pp. D575-D579; doi:10.1093/nar/gk1768.


	This database is a collection of protein-protein transient complexes and domain-domain structures. This issue of the database contains 3020 entries (as of November 2006) of which 561 are two-chain protein complexes and 865 are one-chain proteins parsed into two domains (domain structures). The rest of entries are constructed from PDB files for multi-chain protein complexes by leaving only two interacting chains, (in the database nomenclature designators of those chains are appended to the name of the original PDB file). Detailed description of the database is available here. Each entry consists of the X-ray structure taken from the PDB data bank (in the PDB/ folder), sequence file (in the SEQ/ folder) and the data file (in the INF/ folder) where all relevant information is stored. File names consist of PDB ID and extensions .pdb (X-ray structures), .seq (sequence files or .inf (data files). Current implementation of the database accommodates the following information for each entry, separately for larger (denoted as chain A^) and smaller (chain B) components: Full sequence;* Number of residues; Number of residues on the interface; List of interfacial residues; Number of helices and strands; Absolute (in Å²) and relative interface areas. The database is searchable with respect to majority of the above parameters. Additional search is possible with respect to the PDB ID and protein names. Downloads are possible for both individual entries (as plain text files) and for the whole content or search (checked) result list (as one gzipped file). Supplementary download is available for the subset of the database at 40% sequence identity level (the DPPC40 database). Good luck and feel free to sent suggestions or comment by the clicking Send a comment button. Yes, and do not forget to enable Javascript in your browser, otherwise search engine will not work properly! If usage of the database results to publication please quote the original paper!**
Previous versions of the database	Other relevant resources for protein complexes and domains on Internet:
	*^which, in general, may not coincide with the experimental chain designators in the PDB file. ^ P.J.Kundrotas and E.Alexov (2007) Nucleic Acids Res., v.35, pp. D575-D579; doi:10.1093/nar/gk1768.