Table 1.

URLs and FTP Sites Associated with the CDD Protocols Described in This Paper

https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml	CDD home page
https://www.ncbi.nlm.nih.gov/cdd	Entrez interface to the CDD
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi	CD‐Search Interface
https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml	CDD Help documentation
https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi	BATCH Web CD‐Search interface
https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#BatchRPSBInput	Batch CD‐Search Help documentation
https://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_news.html	CDD News page (for most recent domain database versions)
https://blast.ncbi.nlm.nih.gov/Blast.cgi	BLAST Homepage
https://www.ncbi.nlm.nih.gov/books/NBK279690/	BLAST® Command Line Applications User Manual
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=BlastHelp	BLAST Help documentation
https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.shtml	CDD Cn3d tutorial
https://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml	CDD CDTree: protein domain hierarchy viewer and editor
https://www.ncbi.nlm.nih.gov/sparcle	Entrez interface to SPARCLE
https://www.ncbi.nlm.nih.gov/Structure/sparcle/docs/sparcle_help.html	SPARCLE Help documentation
https://www.ncbi.nlm.nih.gov/books/NBK3837/	Entrez Help documentation
https://ftp.ncbi.nih.gov/pub/mmdb/cdd	CDD FTP site; see the README file for content
https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/	CDD rpsbproc FTP site
https://ftp.ncbi.nih.gov/pub/mmdb/cdd/rpsbproc/README	rpsbproc README file
https://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian	CDD pre‐formatted search databases FTP site
https://ftp.ncbi.nih.gov/blast/executables/LATEST/	NCBI BLAST executables FTP site
https://ftp.ncbi.nih.gov/toolbox	NCBI C++ toolkit distribution FTP site