PROTEIN 3D STRUCTURE

 

Program nameDescription
contacts Reads coordinate files and writes files of intra-chain residue-residue contact data
dichet Parse dictionary of heterogen groups
hmmgen Generates a hidden Markov model for each alignment in a directory
interface Reads coordinate files and writes files of inter-chain residue-residue contact data
profgen Generates various profiles for each alignment in a directory
psiblasts Runs PSI-BLAST given scopalign alignments
scopalign Generate alignments for families in a scop classification file by using STAMP
scoprep Reorder scop classificaiton file so that the representative structure of each family is given first
scopreso Removes low resolution domains from a scop classification file
seqalign Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments
seqsearch Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments
seqsort Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file
seqwords Generate file of hits for scop families by searching swissprot with keywords
siggen Generates a sparse protein signature from an alignment and residue contact data
sigscan Scans a signature against swissprot and writes a signature hits files