Protein domain analysis

Program nameDescription
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
pepcoil Predict coiled coil regions in protein sequences
cathparse Generate DCF file from raw CATH files
domainnr Remove redundant domains from a DCF file
domainseqs Add 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 Remove fragment sequences from DHF files
seqsort Remove ambiguous classified sequences from DHF files
seqwords Generate DHF files from keyword search of UniProt
libgen Generate discriminating elements from alignments
matgen3d Generate a 3D-1D scoring matrix from CCF files
rocon Generate a hits file from comparing two DHF files
rocplot Perform ROC analysis on hits files