|   | PROTEIN DOMAINS | 
Protein domain analysis
| Program name | Description | 
|---|---|
| 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 |