Supplementary Materials For Exploring RNA Conformational Space Under Sparse Distance Restraints
William R. Taylor & Russell S. Hamilton
The two simulation programs are in simgen and simrna. Links to the these will need to be changed to the local copies.
corRNA contains all the scripts used to set-up the sequence data.
strRNA contains the scripts to run the simgen simulations used to find the best perturbation level. The top-level script is code/runs.csh which was run with a parameter 10 (making 10 models). simRNA runs the same simulations for simrna.
strRNAfew runs the series of restraint removals. In each application directory (eg RF00162) executing the script code/runs.csh creats the full deletion series. Similarly in simRNAfew
Due to their large file size the following files are missing from the repository, but are publically available for download.
corRNA/infernal/Rfam.cm (ftp://ftp.ebi.ac.uk/pub/databases/Rfam) corRNA/rfam9full/Rfam.full (ftp://ftp.ebi.ac.uk/pub/databases/Rfam) corRNA/save/seqs/pdb_seqres.txt (ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt) corRNA/seqs/pdb_seqres.txt (ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt)