PROTEIN 3D STRUCTURE

 

Protein tertiary structure

Program nameDescription
psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
contactcount Counts specific versus non-specific contacts in a directory of cleaned protein chain contact files
contacts Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data
domainalign Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file)
domainrep Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first
domainreso Removes low resolution domains from a DCF file (domain classification file)
interface Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data
libgen Generates various types of discriminating elements for each alignment in a directory
rocon Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score
rocplot Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements
seqalign Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits
seqfraggle Removes fragments from DHF files (domain hits files) or other files of sequences
seqsearch Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST
seqsort Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification
seqwords Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt
siggen Generates a sparse protein signature from an alignment and residue contact data
sigscan Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database