PROTEIN 3D STRUCTURE

 

Protein tertiary structure

Program nameDescription
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
scorecmapdir Contact scores for cleaned protein chain contact files
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