Usage

The example and test data could be found in the docker images /MutCov/Example/

1. Prediction the effect of mutation on infectivity

    The MutCov image can be automatically generated using the MutCov script:
    $ MutCov.py --type ACE2 <other arguments>
    <Arguments>
     --Mutation: The amino acid change in S protein such as V503F (substitution), T385del (deletion) and T333_N334insL (insertion). Both single mutation, co-mutation (a virus strain contains multiple mutations separated by plus sign) and multi-mutation (multiple mutations in multiple virus strains separated by comma) is accepted.
    --MDtime: The simulation time of molecular dynamics (ns), default:5
    --nt: The number of threads for Molecular dynamics
    --Model: The PDB ID of ACE2, the model can be choose from '6M0J','6LZG'and '6VW1'.
    --Outpath: Path to output directory
    <Example>
     $ MutCov.py \
        --Mutation V503F, T385del, V503F+T385del \
        --type ACE2 \
        --Model 6M0J \
        --MDtime 5 \
        --nt 64 \
        --Outpath /Path/to/output

2. Prediction the effect of mutation on antigenicity

    $ MutCov.py --type BuiltinAntibody <other arguments>
    <Arguments>
     --Mutation: The amino acid change in S protein such as V503F (substitution), T385del (deletion) and T333_N334insL (insertion). Both single mutation, co-mutation (a virus strain contains multiple mutations separated by plus sign) and multi-mutation (multiple mutations in multiple virus strains separated by comma) is accepted.
    --MDtime: The simulation time of molecular dynamics (ns), default:5
    --nt: The number of threads for Molecular dynamics
    --Model: The PDB ID of Antibody, the model can be choose from '7C01','7BWJ','6W41','6XC2','6XC3_CC12.1','6XC3_CR3022','6XCN','6WPT','7CAH' and '7BZ5'.
    --Outpath: Path to output directory
    <Example>
      MutCov.py \
        --Mutation V503F, T385del, V503F+T385del \
        --type BuiltinAntibody \
        --Model 6M0J \
        --MDtime 5 \
        --nt 64 \
        --Outpath /Path/to/output

3. Prediction the effect of mutation on antigenicity using user-defined antibody

    $ MutCov.py --type CustomizedAntibody <other arguments>
    <Arguments>
     --Mutation: The amino acid change in S protein such as V503F (substitution), T385del (deletion) and T333_N334insL (insertion). Both single mutation, co-mutation (a virus strain contains multiple mutations separated by plus sign) and multi-mutation (multiple mutations in multiple virus strains separated by comma) is accepted.
    --MDtime: The simulation time of molecular dynamics (ns), default:5
    --nt: The number of threads for Molecular dynamics
    --Model: The three-dimensional structures of user-defined antibody complexes with S protein in PDB format
    --Outpath: Path to output directory
    --AntibodySpike: The chain of spike protein in user-defined PDB file
    --AntibodyHeavy: The heavy chain of antibody in user-defined PDB file
    --AntibodyLight: The light chain of antibody in user-defined PDB file
    <Example>
      MutCov.py \
        --Mutation V503F, T385del, V503F+T385del \ \
        --type CustomizedAntibody \
        --Model /Path/to/user-defined/antibody/complexes \
        --MDtime 5 \
        --nt 64 \
        --AntibodySpike A \
        --AntibodyHeavy H\
        --AntibodyLight L \
        --Outpath /Path/to/output