Comparative Modeling databases?

[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!

[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

[Anonymous]

Hello!!

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

Thanks!

[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

[Anonymous]

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

Best,

James

[Anonymous]

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

[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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