Improved contact predictions using the recognition of protein like contact patterns.

• NetSurfP 1.1
• PSIPRED v3.5
• Jackhmmer from HMMER v3.0 or higher
• HHblits from HHsuite v2.0.16
• PSICOV v1.11
• plmDCA asymmetric
• either MATLAB v8.1 or higher
• or MATLAB Compiler Runtime (MCR) v8.1
• (optional: Rosetta v3.5 or weekly built)

MATLAB is needed to run plmDCA. However, if MATLAB is not available you can also use a compiled version of plmDCA. For the compiled version to run you need to provide a path to MCR.

Make sure all dependencies are working correctly and adjust the paths in localconfig.py.

To run PconsC2 use:

./run_pconsc2.py [-c <n_cores>] [-n n_decoys] [-m n_models]
                 [--p_psi <n_psicov_jobs>] [--p_plm <n_plmdca_jobs>]
                 [-f factor] [--norelax] [--nohoms] [--pconsc1]
                 [--rosetta]
                 <hhblits_database> <jackhmmer_database> <sequence file>

• Required:
  • hhblits_database and jackhmmer_database are paths to the databases used by HHblits and Jackhmmer
  • sequence_file is the path to the input protein sequence in FASTA format (only single sequences).
• Optional:
  • n_cores specifies the number of cores to use during computation (default: number of available cores).
  • n_decoys specifies the number of decoy structures generated by Rosetta (default: 2000).
  • n_models is the number of top-ranked models being extracted and eventually relaxed in the end (default: 10).
  • n_plmdca_jobs specifies the number of plmDCA instances run in parallel (default: min(2, n_cores)).
  • n_psicov_jobs specifies the number of PSICOV instances run in parallel (default: min(2, n_cores)).
  • factor determines the number of constraints used to fold the protein, which is: factor * length_of_the_input_sequence (default: 1.0).
  • rosetta flag to run rosetta and produce a structural model based on predicted contacts.
  • norelax is a flag that supresses relaxation of the final models. This can be used to quickly extract structures in the end (only used if rosetta flag specified).
  • nohoms is a flag that ensures that homologous structures are excluded from fragment picking. This is only useful in test cases if the model quality needs to be evaluated with a known structure (only used if rosetta flag specified).
  • --pconsc1 flag runs PconsC1 instead of PconsC2

M.J. Skwark, D. Raimondi, M. Michel, A. Elofsson. Improved contact predictions using the recognition of protein like contact patterns. PloS Computational Biology 10(11):e1003889, 2014.