Enum: AnalysisMethod¶

Methods used to analyse simulation outputs.

URI: https://CCPBioSim.ac.uk/biosim-schema/AnalysisMethod

Permissible Values¶

Value	Meaning	Description
RMSD	None	Calculate the root mean square deviation (RMSD) between distance pairs within…
DSSP	None	Calculate the secondary structure content using the Define Secondary Structur…
GIST	None	Perform the grid inhomogenous solvation theory (GIST), a method for analyzing…
Hydrogen Bonds	None	Calculate hydrogen bonds using geometric criteria
Connolly surface	None	Calculate the Connolly surface area of specified atoms
Radius of Gyration	None	Calculate the radius of gyration for specified atoms
BAR/PBSA	None	BAR/PBSA is a method developed to address inability of alchemical simulations…

Slots¶

Name	Description
analysis_method	Name of the method used to analyse simulation

Identifier and Mapping Information¶

Schema Source¶

from schema: https://CCPBioSim.ac.uk/biosim-schema/

LinkML Source¶

name: AnalysisMethod
description: Methods used to analyse simulation outputs.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
rank: 1000
permissible_values:
  RMSD:
    text: RMSD
    description: Calculate the root mean square deviation (RMSD) between distance
      pairs within selected points, perform best of fit of coordinates to a reference
      first.
    aliases:
    - RMSD
    - root_mean_square_deviation
  DSSP:
    text: DSSP
    description: Calculate the secondary structure content using the Define Secondary
      Structure of Proteins (DSSP) algorithm.
    aliases:
    - DSSP
    - define_secondary_structure_of_proteins
  GIST:
    text: GIST
    description: Perform the grid inhomogenous solvation theory (GIST), a method for
      analyzing the strutre and dyanmics of solvent in the vicinity of a solute molecule.
    aliases:
    - GIST
    - grid_inhomogenous_solvation_theory
  Hydrogen Bonds:
    text: Hydrogen Bonds
    description: Calculate hydrogen bonds using geometric criteria.
    aliases:
    - Hydrogen Bonds
    - hydrogen_bonds
  Connolly surface:
    text: Connolly surface
    description: Calculate the Connolly surface area of specified atoms.
    aliases:
    - Connolly surface
    - connolly_surface
  Radius of Gyration:
    text: Radius of Gyration
    description: Calculate the radius of gyration for specified atoms.
    aliases:
    - Radius of Gyration
    - radius_of_gyration
  BAR/PBSA:
    text: BAR/PBSA
    description: BAR/PBSA is a method developed to address inability of alchemical
      simulations to handle elecronic polarization effects upon ligand transfer from
      water to the protein interior. Used to post-process alchemical simulation trajectories
      to incorporate the polarization effects in a continuum manner.
    aliases:
    - BAR/PBSA
    - bar_pbsa