PROTEIN DOMAINS

Protein domain analysis

Program name	Description
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
pepcoil	Predicts coiled coil regions in protein sequences
cathparse	Generates DCF file from raw CATH files
domainnr	Removes redundant domains from a DCF file
domainseqs	Adds sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
scopparse	Generate DCF file from raw SCOP files
ssematch	Search a DCF file for secondary structure matches
domainalign	Generate alignments (DAF file) for nodes in a DCF file
domainrep	Reorder DCF file to identify representative structures
seqalign	Extend alignments (DAF file) with sequences (DHF file)
seqfraggle	Removes fragment sequences from DHF files
seqsort	Remove ambiguous classified sequences from DHF files
seqwords	Generates DHF files from keyword search of UniProt
libgen	Generate discriminating elements from alignments
matgen3d	Generate a 3D-1D scoring matrix from CCF files
rocon	Generates a hits file from comparing two DHF files
rocplot	Performs ROC analysis on hits files