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.
How to run it:
Make sure all dependencies are working correctly and adjust the paths in
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>
jackhmmer_databaseare paths to the databases used by HHblits and Jackhmmer
sequence_fileis the path to the input protein sequence in FASTA format (only single sequences).
n_coresspecifies the number of cores to use during computation (default: number of available cores).
n_decoysspecifies the number of decoy structures generated by Rosetta (default: 2000).
n_modelsis the number of top-ranked models being extracted and eventually relaxed in the end (default: 10).
n_plmdca_jobsspecifies the number of plmDCA instances run in parallel (default: min(2, n_cores)).
n_psicov_jobsspecifies the number of PSICOV instances run in parallel (default: min(2, n_cores)).
factordetermines the number of constraints used to fold the protein, which is: factor * length_of_the_input_sequence (default: 1.0).
rosettaflag to run rosetta and produce a structural model based on predicted contacts.
norelaxis 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).
nohomsis 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).
--pconsc1flag runs PconsC1 instead of PconsC2