local or remote blast BLASTp against pdb database (formatdb)

Question

[money11gupta]

I want to blastp protein sequence file (>3000 sequences) against PDB database for generating templates for Homology modeling. Please help!!

I tried remote blast and local blast using formatdb but they are showing errors. Please help

Thanks and Regards

Money Gupta

Answer 1

[hpmcwill]

For remote BLAST against PDB use something like (assuming NCBI BLAST+):

blastp -query querySeq.fasta -db pdbaa -remote

For local BLAST you need the database. This can be downloaded from the NCBI FTP site or one of the mirrors (e.g. this one). The 'pdbaa' database is implemented as a mask over the 'nr' database, so you need to download both in order to perform searches.

Due to the nature of PDB chain identifiers, attempting to create a BLAST database from the PDB sequence fasta file(s) provided by the PDB members, will report errors due to the presence of duplicate identifiers. This is due to NCBI BLAST not handing the case sensitivity of the chain Id and thus seeing identifiers such as 3E3Q_A and 3E3Q_a as being the same. While the database can be created using Legacy NCBI BLAST's 'formatdb', this is not recommended since the output can report the wrong sequence in the alignment making it difficult to determine the quality/relevance of the match.

A workaround for this to to add an additional unique component (for example the 'gi' number in the NCBI BLAST databases) or to use a method which does not have problems with the identifiers. Given the size of the PDB databases there is little reason not to use more sensitive similarity search methods such as those provided by the 'SSEARCH' (Smith-Waterman local-local alignment), 'GGSEARCH' (Needleman-Wunsch global-global alignment) and 'GLSEARCH' (global-local alignment) tools in the FASTA suite. As well as the services provided on the FASTA site, additional services are provided by EMBL-EBI which provide both web and Web Services access. For example the FASTA suite is available via:

• Web interface
• REST Web Service
• SOAP Web Service

Helpfully the Web Services include sample clients that can be downloaded and used to access the service.