I just updated our good old server TFmodeller, available at http://www.ccg.unam.mx/tfmodeller,
so that it uses the current collection of 95% non-redundant protein-DNA complexes extracted from the Protein Data Bank. As of Feb 7, 2018, there are 977 such complexes, which can be downloaded.
In addition, I just wrote a Perl client so that predictions can be ordered from the terminal via a SOAP interface, producing XML output which should be easy to parse. The PDB format coordinates of the resulting model are marked-up with
#!/usr/bin/perl -w use strict; use SOAP::Lite; my $URL = 'http://maya.ccg.unam.mx:8080/axis'; my $WSDL = "$URL/TFmodellerService.jws?WSDL"; my $infile = $ARGV[0] || die "# usage: $0\n"; my ($inFASTA,$result); open(FASTA,'<',$infile) ||die "#cannot read $infile\n"; $/ = undef; $inFASTA = ; # slurp close(FASTA); my $soap = SOAP::Lite->uri($URL) ->proxy($URL, timeout => 300 ) ->service($WSDL); eval { $result = $soap->TFmodeller($inFASTA) }; if($@){ die $@ } else{ print $result }
The original Java client can still be found here. Note that the output includes a sequence alignment of query and template with residues contacting DNA nitrogen bases highlighted:
HEADER model 1zrf_A 203 DNACOMPLEX resol=2.10 21 8e-46 REMARK query MILLLSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLG REMARK template KVGNLAFLDVTGRIAQTLLNLAKQ-PDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILK REMARK contacts ........................ ................*........***...*...
Bruno
This server has been replaced by a Docker container that can be found at https://hub.docker.com/repository/docker/eeadcsiccompbio/tfmodeller
ResponderEliminarSorry, the correct URL is https://hub.docker.com/r/eeadcsiccompbio/tfmodeller
ResponderEliminar