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snakemake-cartesian-ddg's Introduction

snakemake-cartesian-ddg

Snakemake pipeline for Rosetta cartesian-ddg application for the prediction of protein stability change (ddG) upon mutation.

Quickstart

  1. Configure paths to your Rosetta binary (ROSETTABIN) and DB (ROSETTADB) in config.yaml.

  2. Place your PDB file in pdb directory and configure target_pdbs in config.yaml.

  3. Prepare mutfiles corresponding to mutations for which you want to measure ddG values.

  4. Configure mutfiles in config.yaml. Note that * means that all mutfiles in the directory will be used.

  5. Run the pipeline.

$ snakemake -pr -j[NUM_CORES]

Pipeline overview

pipeline

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snakemake-cartesian-ddg's Issues

How to deal with result?

The result ddg：
COMPLEX: Round1: WT: -1170.284 fa_atr: -2478.366 fa_rep: 221.594 fa_sol: 1240.103 fa_intra_rep: 3.471 fa_intra_rep_xover4: 58.700 fa_intra_sol_xover4: 63.577 lk_ball_wtd: -121.161 fa_elec: -498.588 hbond_sr_bb: -114.699 hbond_lr_bb: -53.229 hbond_bb_sc: -66.679 hbond_sc: -49.969 dslf_fa13: 0.000 omega: 26.276 fa_dun: 335.973 p_aa_pp: -47.922 yhh_planarity: 0.731 ref: 85.645 sugar_bb: 0.000 rama_prepro: 13.170 cart_bonded: 211.090
APART: Round1: WT: -1143.225 fa_atr: -2436.517 fa_rep: 213.313 fa_sol: 1231.060 fa_intra_rep: 3.471 fa_intra_rep_xover4: 58.700 fa_intra_sol_xover4: 63.577 lk_ball_wtd: -119.669 fa_elec: -497.946 hbond_sr_bb: -114.699 hbond_lr_bb: -53.229 hbond_bb_sc: -66.679 hbond_sc: -49.569 dslf_fa13: 0.000 omega: 26.276 fa_dun: 335.973 p_aa_pp: -47.922 yhh_planarity: 0.731 ref: 85.645 sugar_bb: 0.000 rama_prepro: 13.170 cart_bonded: 211.090
COMPLEX: Round2: WT: -1170.283 fa_atr: -2478.336 fa_rep: 221.602 fa_sol: 1240.078 fa_intra_rep: 3.470 fa_intra_rep_xover4: 58.690 fa_intra_sol_xover4: 63.573 lk_ball_wtd: -121.163 fa_elec: -498.589 hbond_sr_bb: -114.697 hbond_lr_bb: -53.229 hbond_bb_sc: -66.689 hbond_sc: -49.951 dslf_fa13: 0.000 omega: 26.288 fa_dun: 335.955 p_aa_pp: -47.916 yhh_planarity: 0.730 ref: 85.645 sugar_bb: 0.000 rama_prepro: 13.165 cart_bonded: 211.091
APART: Round2: WT: -1143.233 fa_atr: -2436.478 fa_rep: 213.306 fa_sol: 1231.038 fa_intra_rep: 3.470 fa_intra_rep_xover4: 58.690 fa_intra_sol_xover4: 63.573 lk_ball_wtd: -119.670 fa_elec: -497.949 hbond_sr_bb: -114.697 hbond_lr_bb: -53.229 hbond_bb_sc: -66.689 hbond_sc: -49.555 dslf_fa13: 0.000 omega: 26.288 fa_dun: 335.955 p_aa_pp: -47.916 yhh_planarity: 0.730 ref: 85.645 sugar_bb: 0.000 rama_prepro: 13.165 cart_bonded: 211.091
COMPLEX: Round3: WT: -1170.296 fa_atr: -2477.567 fa_rep: 220.846 fa_sol: 1240.426 fa_intra_rep: 3.445 fa_intra_rep_xover4: 58.528 fa_intra_sol_xover4: 63.536 lk_ball_wtd: -121.059 fa_elec: -498.690 hbond_sr_bb: -114.718 hbond_lr_bb: -53.229 hbond_bb_sc: -66.686 hbond_sc: -50.031 dslf_fa13: 0.000 omega: 26.275 fa_dun: 335.748 p_aa_pp: -47.922 yhh_planarity: 0.731 ref: 85.645 sugar_bb: 0.000 rama_prepro: 13.121 cart_bonded: 211.307
APART: Round3: WT: -1143.078 fa_atr: -2435.735 fa_rep: 212.790 fa_sol: 1231.278 fa_intra_rep: 3.445 fa_intra_rep_xover4: 58.528 fa_intra_sol_xover4: 63.536 lk_ball_wtd: -119.622 fa_elec: -497.993 hbond_sr_bb: -114.718 hbond_lr_bb: -53.229 hbond_bb_sc: -66.686 hbond_sc: -49.575 dslf_fa13: 0.000 omega: 26.275 fa_dun: 335.748 p_aa_pp: -47.922

How deal with reult to get ∆∆G？

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