PROTEIN 3D STRUCTURE

Protein tertiary structure

Program name	Description
psiphi	Phi and psi torsion angles from protein coordinates
domainreso	Remove low resolution domains from a DCF file
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
seqsearch	Generate PSI-BLAST hits (DHF file) from a DAF file
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
siggen	Generates a sparse protein signature from an alignment
siggenlig	Generate ligand-binding signatures from a CON file
sigscan	Generate hits (DHF file) from a signature search
sigscanlig	Search ligand-signature library & write hits (LHF file)
contacts	Generate intra-chain CON files from CCF files
interface	Generate inter-chain CON files from CCF files