Comparative Modeling databases?

Member Site Forums Rosetta 3 Rosetta 3 – General Comparative Modeling databases?

  • This topic has 6 replies, 4 voices, and was last updated 8 years ago by Anonymous.
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    • #1098
      Anonymous

        Hello —

        I’m interested in digging deeper into what was presented in this paper:

        Incorporation of evolutionary information into Rosetta comparative modeling
        James Thompson1,*, David Baker1,2,3
        Proteins: Structure, Function, and Bioinformatics
        Volume 79, Issue 8, pages 2380–2388, August 2011
        http://onlinelibrary.wiley.com/doi/10.1002/prot.23046/abstract

        but I can’t figure out how to make constraints or where the databases for formula (1) are to make my own script. The RosettaCON2011 has a tutorial called homology_modeling_with_end_extension which I think demonstrates what I’m interested in, but the files it references:

        DistancePotential.pm:use constant bounds_file => $Bin.’/../cm_data/bounds.txt’;
        DistancePotential.pm:use constant table_data_file => $Bin.’/../cm_data/hhsearch_table.txt’;

        are not included.

        Is this data available yet?

        thanks!

      • #6306
        Anonymous

          Hi Nitroamos,

          It looks like the author of that tutorial forgot to include those files. I’ve attached them to this message, let me know if you have problems downloading them or incorporating them into the scripts. They should be in this path relative to the predict_distances.pl file:

          ../cm_data/bounds.txt
          ../cm_data/hhsearch_table.txt

          Best,

          James

        • #11425
          Anonymous

            Hello!!

            I also need bounds.txt and hhsearch_table.txt files.  Is these data available?

            Thanks!

          • #6308
            Anonymous

              Hi James —

              I had decided to try the forums before bothering you directly, so I’m glad I got your attention anyway! Thanks for the response and the files!

              I can’t find the file predict_distances.pl in either the rosetta distribution or in the tutorials… is it also available?

              thanks!

              Amos.

              ############################################################

              homology_modeling_with_end_extension> ls -R
              .:
              FOR_AUTHORS.txt README.dox rosetta_inputs/ scripts/ starting_files/

              ./rosetta_inputs:
              1N9LA_143_236.region 1N9LA.tpb aat000_03_05.200_v1_3 aat000_09_05.200_v1_3 broker.args comparative_modeling.args t000_.psipred_ss2

              ./scripts:
              cm_scripts/

              ./scripts/cm_scripts:
              bin/ perl_lib/

              ./scripts/cm_scripts/bin:
              amino_acids.py* convert_aln.pl* get_pdb.py* get_pdbs.pl*

              ./scripts/cm_scripts/perl_lib:
              alignment.pm CASP.pm Data/ hhsearch/ JobList.pm Potential.pm Rosetta.pm Text/
              blast.pm CstUtil.pm DistancePotential.pm hhsearch.pm Parallel/ Rosetta/ Statistics.pm TMalign.pm

              ./scripts/cm_scripts/perl_lib/Data:
              Dumper/

              ./scripts/cm_scripts/perl_lib/Data/Dumper:
              Simple.pm

              ./scripts/cm_scripts/perl_lib/hhsearch:
              Util.pm

              ./scripts/cm_scripts/perl_lib/Parallel:
              ForkManager.pm

              ./scripts/cm_scripts/perl_lib/Rosetta:
              AA.pm align_util.pm date_exclusion_scripts/ Fragments.pm JobList.pm PDB/ Protocol.pm TargetFiles.pm
              AlignmentClustering.pm Cartesian.pm date_map.txt Instance.pm Job.pm PDB_Date.pm Sequence.pm Template.pm
              AlignmentPDBmatchAndFix.pm Constraints.pm FileUtil.pm JobGenerator.pm Native.pm PDB.pm Statistics.pm Util.pm

              ./scripts/cm_scripts/perl_lib/Rosetta/date_exclusion_scripts:
              combine_entries.rb get_entries.pl* README

              ./scripts/cm_scripts/perl_lib/Rosetta/PDB:
              AtomRecord.pm

              ./scripts/cm_scripts/perl_lib/Text:
              Template.pm Util.pm

              ./starting_files:
              query.fasta query.hhr

            • #6319
              Anonymous

                Here’s the missing script. Hope that it helps!

                Best,

                James

              • #6396
                Anonymous

                  sorry — i forgot to thank you. i might have some questions later… :-)

                • #11544
                  Anonymous

                    I unforturnately don’t know if those files are still availible, but the ability to add evolutionary information into Rosetta modeling has improved over the years. The current gold standard would be the following papers:

                    https://www.ncbi.nlm.nih.gov/pubmed/26677056

                    https://www.ncbi.nlm.nih.gov/pubmed/26857542

                    https://www.ncbi.nlm.nih.gov/pubmed/26335199

                    https://www.ncbi.nlm.nih.gov/pubmed/24842992

                    https://www.ncbi.nlm.nih.gov/pubmed/24009338

                     

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