MutCov Server

Output

1. Main output directories

    /Path/to/output/
    │──── WildType
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    ├──── MutationType
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    ├──── Result
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    └──── MutCov.log └──── PBDID          ├──── 1.MolecularDynamics          └──── 2.CalculateEnergy ├──── Mutation1 │       ├──── 1.MakeMode1 │       ├──── 2.Align │       ├──── 3.MolecularDynamics │       └──── 4.CalculateEnergy … └──── MutationN ├──── 1.MakeMode1 ├──── 2.Align ├──── 3.MolecularDynamics └──── 4.CalculateEnergy ├──── 1.Binding_Energy │       ├──── 1.Spike_ACE2_BindingEnergy.txt │       ├──── 1.Spike_AntibodyHeavyChain_BindingEnergy.txt │       └──── 1.Spike_AntibodyLightChain_BindingEnergy.txt ├──── 2.Binding_Energy_Contribution │       ├──── 2.Spike_ACE2_BindingEnergy_Contribution.txt │       ├──── 2.Spike_Heavy_BindingEnergy_Contribution.txt │       └──── 2.Spike_Light_BindingEnergy_Contribution.t ├──── 3.Root_Mean_Square_Deviation │       └──── 3.rmsd.txt ├──── 4.Root_Mean_Square_Fluctuation │       └──── 4.rmsf.txt ├──── 5.Solvent_Accessible_Surface │       └──── 5.SASA.txt ├──── 6.Radius_of_Gyration │       └──── 6.RG.txt └──── 7.Hydrogen_Bonds └──── 7.HB.txt

2. The result files

2.1 Spike_Receptor_BindingEnergy.txt:

    he binding energy between ACE2 and its receptor (ACE2, heavy chain of antibody, or light chain of antibody ). It is a text file with a header line, and then one line per mutation with the following 8 fields:
    • MutationName: The mutation ID
    • van der Waal energy: The van der Waal energy between spike and its receptor.
    • Electrostattic energy: The electrostatic energy between spike and its receptor.
    • Polar solvation energy: The polar solvation energy between spike and its receptor.
    • SASA energy: The solvent accessible surface area energy between spike and its receptor.
    • Binding energy: The binding energy between spike and its receptor, including van der Waal energy, electrostatic energy, Polar solvation energy and SASA energy.
    • P-value: The p value of Wilcoxon rank-sum statistic for the binding energy change between wild-type and mutation.
    • FDR: Adjust p-value using Benjamini and Hochberg method

2.2 Spike_Receptor_BindingEnergy_Contribution.txt:

    The contribution of per-residue to the total binding energy between ACE2 and its receptor (ACE2, heavy chain of antibody, or light chain of antibody ). It is a text file with a header line, and then one line per amino acid residue with the following fields:
    • Protein: The protein of amino acid residue
    • Pos: The position of amino acid residue
    • WildType: The contribution of this amino acid residue to the total binding energy in wild-type S protein.
    • Mutation1: The contribution of this amino acid residue to the total binding energy in Mutation1-S protein.
    • …
    • MutationN: The contribution of this amino acid residue to the total binding energy in MutationN-S protein.

2.3 RMSD.txt：

    The root mean square deviation (RMSD) of S protein complexes with its receptors. RMSD describes the molecule’s overall discrepancy with respect to some reference at a specific time. It is a text file with a header line, and then one line per time point with the following fields:
    • Time(ns): The time points of molecular dynamics simulations.
    • Mutation1: The RMSD of Mutation1-S protein complexes with its receptors
    • …
    • MutationN: The RMSD of MutationN-S protein complexes with its receptors.

2.4 RMSF.txt：

    •The root mean square fluctuation (RMSF) of S protein complexes with its receptors. RMSF describes the atom’s variation over the whole trajectory. It is a text file with a header line, and then one line per time point with the following fields:
    • Time(ns): The time points of molecular dynamics simulations.
    • Mutation1: The RMSF of Mutation1-S protein complexes with its receptors
    • …
    • MutationN: The RMSF of MutationN-S protein complexes with its receptors.

2.5 SASA.txt:

    The solvent accessible surface area(SASA) of S protein complexes with its receptors. SASA is the surface area of the complexes that is accessible to a solvent. It is a text file with a header line, and then one line per time point with the following fields:
    • Time(ps): The time points of molecular dynamics simulations.
    • Mutation1: The SASAF of Mutation1-S protein complexes with its receptors
    • …
    • MutationN: The SASA of MutationN-S protein complexes with its receptors.

2.6 RG.txt:

    The radius of gyration(RG) of S protein complexes with its receptors. It is a text file with a header line, and then one line per time point with the following fields:
    • Time(ps): The time points of molecular dynamics simulations.
    • Mutation1: The RG of Mutation1-S protein complexes with its receptors
    • …
    • MutationN: The RG of MutationN-S protein complexes with its receptors.

2.7 HB.txt: ：

    The number of hydrogen bonds (HB) between S protein complexes and its receptors. It is a text file with a header line, and then one line per time point with the following fields:
    • Time(ns): The time points of molecular dynamics simulations.
    • Mutation1: The number of hydrogen bonds between Mutation1-S protein complexes and its receptors
    • …
    • MutationN: The number of hydrogen bonds between MutationN-S protein complexes and its receptors